title: HepG2 Cell : Negative control vs miR-224 vs miR1912 transfected

city: Seoul

first: Myeongjune

last: Go

address: Yonsei-ro,Seodaemun-gu

department: College of Medicine

country: South Korea

institute: Yonsei University

summary: Microarray analysis was performed by transfection of miR-224 and miR-1912 to HepG2 cells to identify the genes regulated by miR-224 and miR-1912. miR-224 is known to down-regulate the mRNA of PCSK9, and miR-1912 was also predicted to down-regulate PCSK9 and verified in our previous experiments. PCSK9 was closely associated with the development of hyperlipidemia by interfering with the recycling of LDLR, and the decrease in PCSK9 and the increase in LDLR gene expression were greater in cells treated with miR 1912.

overall_design: HepG2 cells were cultured on DMEM supplemented with 10% FBS. 2 × 10 5 cells were plated on 1 well of 12-well cell culture plate . miR-224 and miR-1912 were purchased from Ambion Inc, and transfection was performed with Lipofectamine 2000 following the manufacturer's instrument. Then the transfected cells were cultured in DMEM supplemented with 10% FBS and 1% P/S for 24 hours and media was changed to DMEM supplemented with 10% DLPS and 1% P/S. After the day, transfected cells were harvested and RNAs were perpared with miRNeasy micro kit (Qiagen). Analysis was performed for control, miR-224, miR-1912 treated HepG2.

first: Chan-Joo

last: Lee

first: Seung-Hyun


title: COP1 Deficiency in BRAFV600E Melanomas Confers Resistance to Inhibitors of the MAPK Pathway [NGS1609]

status: Public on Jun 24 2025

city: South San Francisco

first: Rohit

last: Reja

state: CA

address: 1 DNA Way

country: USA

institute: Genentech

type: Expression profiling by high throughput sequencing

summary: Aberrant activation of the mitogen-activated protein kinase (MAPK) cascade promotes oncogenic transcriptomes. Despite efforts to inhibit oncogenic kinases, such as BRAFV600E, tumor responses in patients can be heterogeneous and limited by drug resistance mechanisms. Here, we describe patient tumors that acquired COP1 or DET1 mutations after treatment with the BRAFV600E inhibi-tor vemurafenib. COP1 and DET1 constitute the substrate adaptor of the E3 ubiquitin ligase CRL4COP1/DET1, which targets transcription factors, including ETV1, ETV4, and ETV5, for pro-teasomal degradation. MAPK-MEK-ERK signaling prevents CRL4COP1/DET1 from ubiquitinating ETV1, ETV4, and ETV5, but the mechanistic details are still being elucidated. We found that pa-tient mutations in COP1 or DET1 inactivated CRL4COP1/DET1 in melanoma cells, stabilized ETV1, ETV4, and ETV5, and conferred resistance to inhibitors of the MAPK pathway. ETV5, in partic-ular, enhanced cell survival and was found to promote the expression of the pro-survival gene BCL2A1. Indeed, the deletion of pro-survival BCL2A1 re-sensitized COP1 mutant cells to vemu-rafenib treatment. These observations indicate that the post-translational regulation of ETV5 by CRL4COP1/DET1 modulates transcriptional outputs in ERK-dependent cancers, and its inactivation contributes to therapeutic resistance

overall_design: RNA was extracted from A375 cells  for the following genotypes  Wild type (WT)  and COP1 SNP (COP1SNP)

first: R


title: COP1 Deficiency in BRAFV600E Melanomas Confers Resistance to Inhibitors of the MAPK Pathway [CHIP-seq]

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Aberrant activation of the mitogen-activated protein kinase (MAPK) cascade promotes oncogenic transcriptomes. Despite efforts to inhibit oncogenic kinases, such as BRAFV600E, tumor responses in patients can be heterogeneous and limited by drug resistance mechanisms. Here, we describe patient tumors that acquired COP1 or DET1 mutations after treatment with the BRAFV600E inhibi-tor vemurafenib. COP1 and DET1 constitute the substrate adaptor of the E3 ubiquitin ligase CRL4COP1/DET1, which targets transcription factors, including ETV1, ETV4, and ETV5, for pro-teasomal degradation. MAPK-MEK-ERK signaling prevents CRL4COP1/DET1 from ubiquitinating ETV1, ETV4, and ETV5, but the mechanistic details are still being elucidated. We found that pa-tient mutations in COP1 or DET1 inactivated CRL4COP1/DET1 in melanoma cells, stabilized ETV1, ETV4, and ETV5, and conferred resistance to inhibitors of the MAPK pathway. ETV5, in partic-ular, enhanced cell survival and was found to promote the expression of the pro-survival gene BCL2A1. Indeed, the deletion of pro-survival BCL2A1 re-sensitized COP1 mutant cells to vemu-rafenib treatment. These observations indicate that the post-translational regulation of ETV5 by CRL4COP1/DET1 modulates transcriptional outputs in ERK-dependent cancers, and its inactivation contributes to therapeutic resistance.

overall_design: ChIP-seq of ETV5 and 2 histone modifications (H3K4me3, H3K27ac ) in A375 cells was performed on the following genotypes in two replicates: Cop1 wildtype and Cop1 SNP as well as treatment with ERK inhibitor (Vertex11e for 1 h).  We had two pooled input sample as control, one per genotype.


title: COP1 Deficiency in BRAFV600E Melanomas Confers Resistance to Inhibitors of the MAPK Pathway [NGS2569]

overall_design:
ETVs deletion in mouse primary melanocytes for the following genotypes:
Wild type (WT), ETV1 knockout (ETV1 KO), ETV5 knockout (ETV5 KO), and ETV1ETV4ETV5 triple knockout (ETV1ETV4ETV5 KO)


title: Pseudohypoxic stabilization of HIF1α via suppression of cyclophilin D promotes metastasis of melanoma

status: Public on Jun 23 2025

city: ulsan

first: Hye Kyung

last: Park

state: Ulsan

address: 50, UNIST-gil, Eonyang-eup, Ulju-gu, unist-gil 50,  EB110, room402-12

institute: UNIST ( 울산과학기술원)

summary: Stabilization of hypoxia-inducible factor 1 alpha (HIF1α), which is pivotal for regulating cellular responses to insufficient oxygen, is implicated in cancer progression, particularly epithelial-mesenchymal transition and metastasis. Despite its crucial role in tumorigenesis, the precise mechanisms governing HIF1α stabilization are not fully understood. Here, we show that stabilization of HIF1α in metastasizing melanoma under mild hypoxia is regulated primarily by mitochondrial reactive oxygen species (ROS) rather than by reduced oxygen levels. Activated HIF1α suppresses expression of cyclophilin D (CypD), a regulator of the mitochondrial permeability transition pore (mPTP), as a reciprocal regulatory mechanism to sustain HIF1 signaling via upregulation of microRNAs miR-23a/27a. Reduced expression of CypD closes the mPTP to increase mitochondrial calcium accumulation and oxidative phosphorylation, thereby boosting ROS production to inactivate a prolyl hydroxylase and establish a psuedohypoxic state. This HIF1-reinforced and mitochondria-driven pseudohypoxic induction is essential for maintaining HIF1 signaling under conditions of mild hypoxia or temporary elevation of oxygen levels during melanoma metastasis. Overexpression of CypD reversed the pseudohypoxic state, and potently inhibited melanoma metastasis. Thus, mitochondria-driven pseudohypoxic induction is critical for sustaining HIF1 signaling in metastasizing cancer cells, and can be exploited to develop anti-metastatic therapies

overall_design: RNA-seq profiling of wild-type B16F10 cells and ppif knockout or overexpressing stable cell lines after 24 hours under hypoxic or normoxic conditions.

first: Byoung Heon

last: Kang

first: Hye-Kyung


title: COP1 Deficiency in BRAFV600E Melanomas Confers Resistance to Inhibitors of the MAPK Pathway

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Regulation of pancreatic cancer migration by signal convergence in the epigenome [ChIP-Seq]

status: Public on Jun 26 2025

city: Stuttgart

first: Steven

middle: A

last: Johnsen

address: Auerbachstrasse 112

country: Germany

institute: Robert Bosch Center for Tumor Diseases

summary: Pancreatic ductal adenocarcinoma (PDAC) is frequently diagnosed at an advanced, metastatic stage. PDAC treatment is challenging due to high tumor cell plasticity, tumor heterogeneity, and a dense tumor microenvironment (TME), all of which strongly influence tumor metastasis. While mutations in the KRAS gene characterize PDAC, inflammatory signaling from the TME accelerates tumor progression, metastasis, and therapy resistance. While individual roles of oncogenic and inflammatory signaling in promoting PDAC progression have been studied extensively, the epigenetic and transcriptional mechanisms by which they function combinatorially in metastasis remain unclear. Our study elucidates how inflammatory TNFα and oncogenic MAPK signaling pathways converge to control PDAC cell migration through activation of NF-κB and AP1 transcription factors, respectively. Combining single-cell RNA sequencing (scRNAseq) analyses, multiplex immunofluorescence staining, in vitro, and in vivo studies, we unveil that the simultaneous activation of these pathways with TNFα and EGF induces the expression of specific genes associated with cell motility and migration. We show that combinatorial induced genes are co-bound by FOSL1 and RELA. Remarkably, inhibition of NF-κB transcriptional activity using glucocorticoid receptor (GR) mixed agonists significantly reduces RNA polymerase II across the target genes and inhibits cell migration. These findings highlight the potential of GR agonists, commonly utilized to alleviate chemotherapy side effects, in mitigating PDAC tumor migration. Our study offers promising avenues for developing mechanism-based therapeutic strategies in PDAC management.

overall_design: To explore the epigenetic mechanism by which inflammatory NF-κB signaling converges with oncogenic MAPK signaling to regulate cell migration in pancreatic cancer, we conducted ChIP-seq on the PDAC cell lines AsPC-1 and L3.6pl. The experiment was performed under control conditions and after treatment with EGF (to activate oncogenic signaling), TNFα (to activate inflammatory signaling), and a glucocorticoid agonist (GR). Additionally, siRNA-mediated depletion of the transcription factors FOSL1 and RELA was included.

first: Joana

middle: E

last: Aggrey-Fynn


title: AEBP1-GLI1 pathway attenuates the FACT complex dependency of bladder cancer cell survival.

status: Public on Jun 20 2025

city: Nagakute

first: Kenji

last: Kasai

state: Aichi

address: 1-1 Yazakokarimata

department: Pathology

country: Japan

institute: Aichi Medical University School of Medicine

summary: AEBP1 expression predicts a poor prognosis of bladder cancer patients, while its role has not been fully understood. We here show that the expression of AEBP1 was correlated with GLI transcriptional factors, leading to limit the SSRP1/SUPT16H (FACT) complex-dependency of bladder cancer cells.

overall_design: AEBP1-highly expressing human bladder cancer cell line 5637 was used for the RNA-seq experiment: cells were transfected with either AEBP1-specific siRNA siAEBP1-1 or its control siControl. 72 hours after transfection, cells were harvested for RNA exraction. The gene expression profile was then analyzed using data obtained from the RNA-seq of triplicate samples.

first: Norika

last: Yamada

first: Haruka

last: Kurosu

first: Naoto

last: Sassa


title: Fate (or state) of CA2 neurons in a mineralocorticoid receptor knockout.

city: Research Triangle Park

first: Serena

middle: M

last: Dudek

state: NC

address: 111 TW Alexander Dr.

department: Neurobiology

institute: NIEHS

summary: Area CA2 has emerged as a functionally and molecularly distinct part of the hippocampus, and in mice, its development as such appears to rely critically on the mineralocorticoid receptor (MR; Nr3c2). To better understand the fate (or state) of the neurons resulting from MR conditional knockout, we used a spatial transcriptomics approach. We found that without MRs, ‘CA2’ neurons acquire a CA1-like molecular and anatomical phenotype.

overall_design: compare hippocampal subregions in WT and MRKO mouse brain

first: Erin

last: Harris

first: Tian

middle: Y

last: Wang

first: Basak

last: Kandemir

first: James

last: Ward


title: Expanding the diversity of bacterial DNA partitioning: A CTP-independent ParABS system for plasmid partitioning in Streptomyces

status: Public on Jun 22 2025

city: Norwich

first: Tung

middle: Ba  Khanh

last: Le

state: Norfolk

address: Colney Lane

department: Department of Molecular Microbiology

country: United Kingdom

institute: John Innes Centre

summary: The ATP- and CTP-dependent ParA-ParB-parS segrosome is a macromolecular complex that segregates chromosomes/plasmids in most bacterial species. CTP binding and hydrolysis enable ParB to slide along DNA and to bridge and condense DNA, thereby dictating the size and dynamics of the tripartite ParABS complex. Several other evolutionarily distinct systems can also segregate DNA, although the full diversity of bacterial DNA partition systems remains unknown. Here, we identify a CTP-independent ParABS system that maintains the conjugative plasmid SCP2 in the filamentous bacterium Streptomyces coelicolor. We demonstrate that an SCP2 ParB-like protein, ParT, loads onto DNA at an 18-bp parS site and diffuses away to the adjacent DNA despite lacking an apparent CTPase domain and detectable NTPase activity. We further show that parS DNA facilitates ParT transition from loading to a diffusing state, allowing ParT to accumulate on DNA, and that ParT activates the ATPase activity of its cognate partner protein, ParA. Additionally, we identify numerous structural homologs of ParT, suggesting that CTP-independent diffusion on DNA might be more common than previously recognized. Overall, our findings reveal a CTP-independent DNA translocation as an alternative and unexpected mechanism for assembling a bacterial DNA segregation complex and suggest that CTP binding and hydrolysis are not universal features of ParABS-like systems.

overall_design: Chromatin-immunoprecipitation with deep sequencing experiments (ChIP-seq) were performed on Streptomyces coelicolor strains grown in liquid cultures (see the supplementary Materials and Methods for the exact treatment that were applied to each strain).

first: Kirill

middle: V

last: Sukhoverkov

middle: B


title: Integrated multi-omics analysis of liver metabolic dysregulation in ACE2 knockout mice

city: Jining

first: Shuai

last: Xiao

address: No. 1068 Xueyuan Avenue, Shenzhen University Town, Xili, Nanshan District, Shenzhen, China University Town of Shenzhen, Xili Nanshan, Shenzhen 518055, P.R.China

country: China

institute: Jining First People's Hospital Affiliated to Shandong First Medical University

summary: This study reveals the molecular mechanisms of liver metabolic dysregulation in ACE2 knockout (ACE2KO) mice through multi-omics analysis. ACE2 deficiency exacerbates lipid accumulation, disrupts RAS balance, and induces hepatocyte injury and inflammation. Integrated multi-omics analysis identified numerous differentially expressed genes, proteins, and metabolites, highlighting the PPAR signaling pathway as a central regulatory hub. ACE2 deletion also impairs detoxification and antioxidant balance, creating a self-reinforcing oxidative injury cycle. These findings provide new insights into the mechanisms and therapeutic targets of ACE2-related liver diseases.

overall_design: RNA-seq profiling of 8-week-old male ACE2 knockout (ACE2KO) mice and age-matched C57BL/6J wild-type control mice.


title: MET Pathway Inhibition Increases Chemo-Immunotherapy Efficacy in Small Cell Lung Cancer

city: Barcelona

first: Júlia

last: Perera-Bel

address: Doctor Aiguader, 88

department: MARData-BU

country: Spain

institute: Hospital del Mar Research Institute

summary: Chemotherapy in combination with immunotherapy offers limited benefit in advanced Small Cell Lung Cancer (SCLC). This study explores the potential of combining MET pathway inhibition with chemo-immunotherapy for treating advanced SCLC. MET pathway activation triggers epithelial-mesenchymal transition, fostering chemoresistance and potentially undermining the efficacy of immunotherapy. In a SCLC mouse model, MET inhibition added to chemo-immunotherapy (anti-PD-L1) reduced tumor growth and extended survival by reshaping the tumor microenvironment, decreasing suppressive myeloid cells, and promoting an effective immune response. Analysis of patient samples revealed that myeloid-enriched immune infiltrates during chemo-immunotherapy might contribute to treatment resistance. Notably, elevated serum hepatocyte growth factor (HGF) levels were associated with a mesenchymal and inflamed phenotype, indicating that this subgroup of patients could potentially benefit from MET inhibitor (METi)-based therapeutic strategies.

overall_design: B6129SF1/J mice bearing subcutaneous SCLC tumours (KP1 or 5B) were randomly assigned to receive a) Cisplatin; b) Cisplatin + anti-PD-L1; c) Cisplatin + anti-PD-L1 + savolitinib. Animals were sacrificed at day 19 (KP1) or day 22 (5B) and tumours were extracted and processed for the transcriptomic assessment through RNAseq.

first: Raúl

last: Del Rey-Vergara

first: Miguel

last: Galindo-Campos

first: Pedro

last: Rocha

first: Ana

last: Rovira

first: Edurne

last: Arriola


title: Nanosilicates Promote Angiogenesis Through Activation of ROS-Mediated WNT/β-Catenin Pathway

city: College Station

first: Akhilesh

last: Gaharwar

state: TX

address: 101 Bizzell St

department: BME

institute: Texas A&M University

summary: Scaffold vascularization plays a pivotal role in the wound healing process, facilitating the recruitment of endogenous progenitor cells and delivering crucial signaling molecules that promote cellular invasion, angiogenesis, and neo-tissue formation. In this study, we introduce nanosilicates as pro-angiogenic biomaterials that can prime endogenous cells to expedite angiogenesis and graft vascularization in vivo. Characterized by their mineral-based two-dimensional (2D) structure and extensive surface area, nanosilicates are efficiently internalized by endothelial cells, leading to augmented cellular migration and the formation of tubular structures. Through whole transcriptome sequencing, we elucidated that nanosilicates activate the canonical Wnt pathway through hypoxia-induced ROS production. In vivo investigations further corroborate the pro-angiogenic efficacy of nanosilicates-loaded biomaterials. This study posits nanosilicates as a potential pro-angiogenic adjunct in the design of biomaterials for in situ tissue regeneration.

overall_design: Nanosilicates enhance scaffold vascularization by activating Wnt signaling, promoting angiogenesis for tissue regeneration.

first: Giriraj

middle: K

last: Lokhande

first: Kanwar

last: Abhay Singh

first: Shounak

last: Roy

first: John

last: Soukar

first: Anna

last: Kersey

first: Saptarshi

last: Biswas

first: Raza

middle: R

last: Syed

middle: L

last: Keller

first: Kayla

middle: J

last: Bayless

first: Irtisha

last: Singh


title: STAMP: Single-Cell Transcriptomics Analysis and Multimodal Profiling through Imaging

city: Memphis

first: Jasmine

last: Plummer

state: TN

address: 262 Danny Thomas Pl

department: Developmental Neurobiology

institute: St. Jude Children's Research Hospital

platform_organism:
Homo sapiens
Mus musculus
synthetic construct


title: Dissecting the enhancer gene regulatory network in early Drosophila spermatogenesis

city: Heidelberg

first: Ingrid

last: Lohmann

address: Im Neuenheimer Feld 230

institute: Centre for Organismal Studies Heidelberg

summary: Cellular decision-making and tissue homeostasis are governed by transcriptional networks shaped by chromatin accessibility. Using single-nucleus multi-omics, we jointly profiled gene expression and chromatin accessibility in 10,335 cells from the Drosophila testis apical tip. This enabled inference of 138 cell type-specific enhancer regulons (eRegulons) using SCENIC+. We functionally validated key transcription factors (TFs), including ovo and klumpfuss (klu), known from other stem cell systems but not previously linked to spermatogenesis. CRISPR-mediated knockout revealed their essential roles in germline stem cell (GSC) regulation, and we provide evidence that they co-regulate shared targets through overlapping enhancer elements. We further uncovered a critical role for canonical Wnt signaling, with Pangolin/Tcf activating lineage-specific targets in the germline, soma, and niche. The Pan eRegulon links Wnt activity to cell adhesion, intercellular signaling and GSC maintenance. Together, our study defines the enhancer-driven regulatory landscape of early spermatogenesis and reveals conserved, combinatorial mechanisms of niche-dependent stem cell control.

overall_design: Dmel w1118 were raised at 25°C and virgins were collected. Testes from 1 day old flies were dissected and testis apical tips were cut and flashfrozen in liquid nitrogen. Finally, testis tips were pooled and nuclei were isolated according to protocol.

first: Patrick

last: van Nierop y Sanchez

first: David

last: Ibberson

first: Laura Zoe

last: Kreplin


title: Gpr37 contributes to inflammation-induced GI dysmotility by regulating enteric reactive gliosis.

city: Stanford

first: Julia

last: Kaltschmidt

address: 288 Campus Drive

department: Neurosurgery

institute: Stanford University

summary: The enteric nervous system (ENS) is contained within two layers of the gut wall and is made up of neurons, immune cells, and enteric glia cells (EGCs) that regulate gastrointestinal (GI) function. EGCs in both inflammatory bowel disease (IBD) and irritable bowel syndrome (IBS) change in response to inflammation, referred to as reactive gliosis. Whether EGCs restricted to a specific layer or region within the GI tract alone can influence intestinal immune response is unknown. Using bulk RNA-sequencing and in situ hybridization, we identify G-protein coupled receptor, Gpr37, as a gene expressed only in EGCs of the myenteric plexus, one of the two layers of the ENS. We show that Gpr37 contributes to key components of LPS-induced reactive gliosis including activation of NF-kB and IFN-y signaling and response genes, lymphocyte recruitment, and inflammation-induced GI dysmotility. Targeting Gpr37 in EGCs presents a potential avenue for modifying inflammatory processes in the ENS.

overall_design: Transcriptional profiles of EGCs from: (1) all four regions and layers of the GI tract in adult Plp1eGFP mice, n= 5-6. (2)  LPS- or PBS-treated Plp1eGFP mice in the SI MP and colon MP, n=4, 2-hour timepoint. (3) LPS- or PBS-treated Gpr37WT; Plp1eGFP and Gpr37-/-; Plp1eGFP mice in the SI MP and colon MP, n=4-6, 24-hour timepoint.

first: Keiramarie

last: Robertson

first: Oliver

last: Hahn

first: Beatriz

middle: G

last: Robinson

first: Arwa

middle: T

last: Faruk

first: Mathangi

last: Janakiraman

first: Hong

last: Namkoong

first: Kwangkon

last: Kim

first: Jiayu

last: Ye

first: Estelle

last: Spear Bishop

first: Randy

last: Hall

first: Tony

last: Wyss-Coray

first: Laren

middle: S

last: Becker


title: Coupling chromosome organization to genome segregation in Archaea

first: Tung

last: Le

summary: Chromosome segregation is a fundamental process in all life forms and requires coordination with genome organization, replication and cell division. The mechanism that mediates chromosome segregation in archaea remains enigmatic, despite the centre-stage role assumed by these organisms in the discourse about the origin of eukaryotes. Previously, we identified two proteins, SegA and SegB, which form a minimalist chromosome partition machine in Sulfolobales. Here we uncover patterns and mechanisms that the SegAB system employs to link chromosome organization to genome segregation. Deletion of the genes causes growth and chromosome partition defects. ChIP-seq investigations revealed that SegB binds to multiple sites scattered across the chromosome, but mainly localised close to the segAB locus in most of the examined archaeal genera. The sites are predominantly present in intragenic regions. Recent chromosome conformation studies have shown that the chromosome of Sulfolobales members is organised into two spatially segregated compartments, designated A and B. Interestingly, SegB sites are predominantly located in the A compartment, whose shaping factors have remained elusive so far. We show that SegB coalesces into multiple foci through the nucleoid, exhibiting a biased localisation towards the cell periphery, which hints at potential tethers to the cell membrane. This clue is further strengthened by the structural similarities of SegB orthologues with predicted b-helix domains to membrane-associate proteins, including the distant bactofilin. Atomic force microscopy experiments provided mechanistic insights into how SegB binds DNA and uncovered short-range DNA compaction and long-range looping of distant sites by SegB. These activities point to a significant role for SegB in chromosome condensation that in turn enables genome segregation. Collectively, our data put forward SegAB as important players in bridging chromosome organization to genome segregation in archaea.

overall_design: ChIP-seq of exponential phase S. acidocaldarius cells in wild type versus ΔsegB strains, using anti-SegB polyclonal antibody

first: Parul

last: Pal

first: BK Tung

first: Daniela

last: Barillà


title: Mouse lung injury-repair induces Ntrk2-tk in CAP1 endothelial cells (scATAC-Seq)

city: Cincinnati

first: Jichao

last: Chen

state: OH

address: 3333 Burnet Avenue

institute: Cincinnati Children's Hospital

summary: The pulmonary capillary endothelial cells (ECs) consist of two populations, CAP1 and CAP2; how each population reacts to diverse tissue injury is incompletely understood. Using single-cell multiome and genetic lineage tracing, we characterize the induction and function of a truncated isoform of Ntrk2, Ntrk2-tk (lacking the tyrosine kinase domain), in multiple lung injury models in mice. Upon Sendai parainfluenza infection, Ntrk2-tk is activated in CAP1 across the whole lung after the initial interferon response, associated with increased intronic accessibility, and persists for weeks after injury. Ntrk2-tk ECs arise from CAP1 but not CAP2, traced by KitCreER and Car4CreER, respectively, and proliferate and give rise to CAP1 but not CAP2, as traced by Ntrk2CreER. EC-specific deletion of Ntrk2 has little molecular and cellular consequences in response to Sendai and H3N2 viral infection. Our data identifies Ntrk2-tk as an EC marker of lung injury-repair and enhances our understanding of EC heterogeneity.

overall_design: FACS purified lung cells (endothelial and mesenchymal) in PBS and Sendai-infected mouse lungs

first: Celine

last: Kong


title: Spatiotemporal organisation of residual disease in mouse and human BRCA1-deficient mammary tumors and breast cancer

status: Public on Jun 19 2025

city: Bern

first: Sven

last: Rottenberg

address: Länggassstrasse 122

country: Switzerland

institute: University of Bern

summary: Breast cancer remains one of the prominent causes of death worldwide. Although chemotherapeutic agents often result in substantial reduction of primary or metastatic tumors, remaining drug-tolerant tumor cell populations, known as minimal residual disease (MRD), pose a significant risk of recurrence and therapy resistance. In this study, we describe the spatiotemporal organisation of therapy response and MRD in BRCA1;p53-deficient mouse mammary tumors and human clinical samples using a multimodal approach. By integrating single-cell RNA sequencing, spatial transcriptomics, and imaging mass cytometry across multiple treatment timepoints, we characterise dynamic interactions between tumor cell subpopulations and their surrounding microenvironment. Our analysis identifies a distinct, drug-tolerant epithelial-mesenchymal transition (EMT) cancer cell population, which exhibits a conserved expression program in human BRCA1-deficient tumors and significantly correlates with adverse clinical outcomes. We further reveal the spatial distribution of residual EMT-like tumor cells within specific anatomical niches, providing a framework for understanding the persistence of MRD and potential therapeutic vulnerabilities. These findings yield a comprehensive molecular roadmap of MRD, opening new avenues for therapeutic strategies targeting EMT-driven drug tolerance and tumor relapse.

overall_design:
Spatial transcriptomics: Mammary tumors derived from the K14cre;Brca1F/F;Trp53F/F (KB1P) mouse model were transplanted into the fourth mammary fat pad of syngeneic FVB/NJ mice. To minimise genetic variability, all tumors originated from two parental tumors that were subdivided before transplantation. Tumor-bearing mice were sacrificed at baseline or treated with a single dose of cisplatin or TAC therapy (doxorubicin, docetaxel, and cyclophosphamide). Spatial transcriptomics (ST) was applied to primary (n = 10), residual (n = 16), recurrent (n = 4) tumor sections, and healthy mammary glands (n = 2), (total n = 32). Residual tumors were collected at 7 (TAC: n = 2, Cisplatin: n = 2) or 12 days (TAC: n = 4, Cisplatin: n = 3) post-treatment. Recurrent tumors were harvested upon regrowth (TAC: n = 2, Cisplatin: n = 2). All animal experiments were approved by the Animal Ethics Committee of the canton of Bern (Switzerland) and are in accordance with the current Swiss Acts on Animal Experimentation. Additionally, tumor samples from five women carrying germline BRCA1 mutations were collected at surgery. ST was performed on primary (n = 2) and residual (n = 3) tumors (after neoadjuvant chemotherapy). Patients were treated at Geneva University Hospitals in Switzerland. The study was approved by the local ethical committee under protocol CCER 2019-00004, and all donors were coded.
scRNA-seq: Mammary tumors derived from the K14cre;Brca1F/F;Trp53F/F (KB1P) mouse model were transplanted into the fourth mammary fat pad of syngeneic FVB/NJ mice. To minimise genetic variability, all tumors originated from two parental tumors that were subdivided before transplantation. Tumor-bearing mice were sacrificed at baseline or treated with a single dose of TAC therapy (doxorubicin, docetaxel, and cyclophosphamide). Single-cell RNA sequencing was performed on primary (n = 3) and residual (n = 3) tumors and collected 12 days post-treatment. All animal experiments were approved by the Animal Ethics Committee of the canton of Bern (Switzerland) and are in accordance with the current Swiss Acts on Animal Experimentation.

first: Demeter

last: Túrós

first: Morgane

last: Decollogny

first: Astrid

last: Chanfon

first: Myriam

last: Siffert

first: Lou

last: Romanens

first: Jean-Christophe

last: Tille

first: Intidhar

last: Labidi-Galy

first: Alberto

last: Valdeolivas


title: Restorative effect of adipose tissue-derived stem cells (ADSCs) on palmitic acid (PA)-activated IMS/N hepatic stellate cells

city: Kanazawa

first: Alessandro

last: Nasti

state: Ishikawa

address: 13-1 Takaramachi, Medical Building B, b34

department: Graduate School of Medical Sciences

institute: Kanazawa University

summary: The restorative indirect effect of ADSCs on activated IMS/N hepatic stellate cells was evaluated by gene expression analysis (DNA microarray). IMS/N were stimulated by palmitic acid (PA), and the effect of media derived by cell culture of ADSCs was verified by gene expression analysis.

overall_design: IMS/N cells were cultured with or without PA, and with or without media derived from the cell culture of ADSCs. Then total RNA was isolated from IMS/N cells. Total RNAs was used for DNA microarray analysis and analyzed the gene expression. Quantile normalization was performed. Gene list of upregulated genes in IMS/N plus PA condition (downregulated in IMS/N condition) is obtained and used for MetaCore Enrichment Pathway analysis. Furthermore, gene list of upregulated genes in IMS/N plus PA condition (downregulated in IMS/N plus PA plus ADSCs' media condition) is obtained and used for MetaCore Enrichment Pathway analysis.

first: Norihiko

last: Ogawa

first: Akihiro

last: Seki

first: Ho

last: Yagi

first: Hiiro

last: Inui

first: Hiroki

last: Nomura

first: Hidetoshi

last: Nakagawa

first: Kouki

last: Nio

first: Hajime

last: Takatori

first: Tetsuro

last: Shimakami

first: Masao

last: Honda

first: Shuichi

last: Kaneko

first: Yoshio

last: Sakai

first: Taro

last: Yamashita


title: Unveiling Aging Heterogeneities in Human Dermal Fibroblasts via Nanosensor Chemical Cytometry

city: Suwon-si

first: Youngho

last: Song

state: Gyeonggi-do

address: Room 25302, Engineering Building 2, 2066 Seobu-ro, Jangan-gu

department: School of Chemical Engineering

institute: Sungkyunkwan University

summary: To investigate aging heterogeneity in tissue-regeneration cells, we conducted RNA-seq analysis of human dermal fibroblasts (hDFs) at two distinct aging stages: passage 5 (p5) and passage 15 (p15). hDFs were cultured under standard conditions, and total RNA was extracted for sequencing. Transcriptomic profiling was performed to identify differentially expressed genes associated with cellular aging. This RNA-seq dataset was used to validate the phenotypic changes observed via a label-free, nondestructive single-cell analytics platform called nanosensor chemical cytometry (NCC). The integrated analysis revealed that transcriptomic aging signatures correspond with aging phenotypes such as changes in cell size, shape, refractive index, and H2O2 efflux. This dataset provides insight into the molecular mechanisms underlying cell aging and supports the development of predictive models for therapeutic performance in regenerative medicine.

overall_design: RNA-seq analysis was performed to compare transcriptomic changes in human dermal fibroblasts (hDFs) at two distinct aging stages: passage 5 (p5) and passage 15 (p15). Four biological replicates were included for each passage group to identify differentially expressed genes associated with cellular aging.

first: Inwoo

last: Seo

first: Changyu

last: Tian

first: Jiseon

last: An

first: Seongcheol

last: Park

first: Jiyu

last: Hyun

first: Seunghyuk

last: Jung

first: Hyun Su

first: Hyun-Ji

first: Suk Ho

last: Bhang

first: Soo-Yeon

last: Cho


title: Mouse lung injury-repair induces Ntrk2-tk in CAP1 endothelial cells (scRNA-Seq)

first: Jichao

last: Chen

overall_design: FACS purified lung cells (epithelial, mesenchymal, immune, and endothelial) in PBS, control, and Ntrk2 mutant mice (Sendai- or H3N2 Influenza A infected)

first: Celine

last: Kong


title: Restorative effect of adipose tissue-derived stem cells (ADSCs) on IL17A-activated IMS/N hepatic stellate cells

first: Alessandro

last: Nasti

summary: The restorative indirect effect of ADSCs on activated IMS/N hepatic stellate cells was evaluated by gene expression analysis (DNA microarray). IMS/N were stimulated by IL17A, and the effect of media derived by cell culture of ADSCs was verified by gene expression analysis.

overall_design: IMS/N cells were cultured with or without IL17A, and with or without media derived from the cell culture of ADSCs. Then total RNA was isolated from IMS/N cells. Total RNAs was used for DNA microarray analysis and analyzed the gene expression. Quantile normalization was performed. Gene list of upregulated genes in IMS/N plus IL17A condition (downregulated in IMS/N condition) is obtained and used for MetaCore Enrichment Pathway analysis. Furthermore, gene list of upregulated genes in IMS/N plus IL17A condition (downregulated in IMS/N plus IL17A plus ADSCs' media condition) is obtained and used for MetaCore Enrichment Pathway analysis.

first: Norihiko

last: Ogawa

first: Akihiro

last: Seki

first: Ho

last: Yagi

first: Hiiro

last: Inui

first: Hiroki

last: Nomura

first: Hidetoshi

last: Nakagawa

first: Kouki

last: Nio

first: Hajime

last: Takatori

first: Tetsuro

first: Masao


title: Catalytic inhibition of KAT6/KAT7 enhances the efficacy and overcomes primary and acquired resistance to Menin inhibitors in MLL leukaemia

city: Melbourne

first: Mark

last: Dawson

address: 305 Grattan Street

department: Cancer Research

country: Australia

institute: Peter MacCallum Cancer Centre

overall_design: Refer to individual Series


title: Characteristics of liver tissues of MASH compared to those of Simple Steatosis mice.

summary: Characteristics of hepatocytes of Metabolic Dysfunction-Associated Steatohepatitis (MASH) mice were compared compared to those of Simple Steatosis (SS) mice in the context of UPR response.

overall_design: Characteristics of hepatocytes of Metabolic Dysfunction-Associated Steatohepatitis (MASH) mice compared to those of Simple Steatosis (SS) mice. MASH or simple steatosis mice were established by feeding an Atherogenic high-fat diet or HFD-60, correspondingly, for 12 weeks, and hepatocytes were obtained for the following analysis. Normalized Log-Transformed Gene Expressions for Genes related to Perk mediated UPR response, to Atf6 mediated UPR response, and to Ire1 mediated UPR response were obtained.

last: Shimakami

last: Honda

first: Shuichi

last: Kaneko

first: Yoshio

last: Sakai

first: Taro

last: Yamashita


title: APOE4 impacts cortical neurodevelopment and alters network formation in human brain organoids

city: San antonio

first: Karina

middle: Kaisha

last: Meyer-Acosta

address: One UTSA circle

department: Neuroscience, developmental, and regenerative biology

institute: University of Texas at San Antonio

summary: Apolipoprotein E4 (APOE4) is the leading genetic risk factor for Alzheimer’s disease. While most studies examine the role of APOE4 in aging, APOE4 causes persistent changes in brain structure as early as infancy and is associated with altered functional connectivity that extends beyond adolescence. Here, we used human induced pluripotent stem cell (iPSC) derived cortical and ganglionic eminence organoids (COs and GEOs) to examine APOE4’s influence during cortical development of excitatory and inhibitory neurons. We show that APOE4 reduced cortical neurons and increased glia by promoting gliogenic transcriptional programs. In contrast, increased proliferation and differentiation of GABAergic progenitors resulted in early and persistent increases in GABAergic neurons. Multi-electrode array recordings in assembloids revealed that APOE4 disrupted neural network function resulting in heightened excitability and synchronicity. Together, our data provides new insights on how APOE4 influences cortical neurodevelopmental processes and network formation.

overall_design: To investigate the neurodevelopmental role of APOE4, we performed bulk RNA-sequencing APOE4 and APOE3 organoids. 2 isogenic iPSC pairs were used. Isogenic female line was derived from APOE3/3 healthy control converted to APOE4/4, and male isogenic line was derived from APOE4/4 alzheimer’s disease male converted to APOE3/3. Each line, 2 APOE3/3 and 2 APOE4/4, were used to generate cortical and ganglionic eminence organoids (COs and GEOs, respectively), undergoing 2 independent replicates. We harvest mRNA at two time points (days in vitro, DIV) 30 and 120 for RNAseq. 4 different comparisons, which we call conditions, were made (COs and GEOs, at both 30 and 120 DIV). For example, samples collected for 1 condition, COs at 30 DIV: 1 sample was collected x 2 replicates for each iPSC line. This results in 2 APOE3/3 samples, 2 APOE4/4 samples for each iPSC line, resulting in 4 APOE3/3 and 4 APOE4/4 samples total (2 iPSC line pairs) for this condition. All samples were ran at the same time. For all 4 conditions, 16 APOE3/3 samples, 16 APOE4/4 samples were collected for a total of 32 samples.

last: K. Meyer-Acosta

first: Eva

last: Diaz Guerra

first: Parul

last: Varma

first: Adyasha

last: Aruk

first: Sara

last: Mirsadeghi

first: Aranis

last: Muniz Perez

first: Yousef

last: Rafati

first: Ali

last: Hosseini

first: Vanesa

last: Nieto-Estevez

first: Michele

last: Giugliano

first: Christopher

last: Navara

first: Jenny

last: Hsieh


title: Adaptive responses of yeast to cell wall stress

city: Burjassot

first: Jose

middle: E.

last: Perez-Ortin

state: Valencia

address: Dr. Moliner 50

department: Bioquimica y Biologia Molecular

institute: Universitat de Valencia

summary: To better understand the roles of SR (calculated from the nascent TR by dividing it by cell volume) (Pérez-Ortín, BioEssays 2013), and mRNA stability in stress adaptation, we investigated the yeast cell wall stress response and compared it with other stress responses using the GRO method. In this study, we analyzed genome-wide changes in RNA abundance to determine how synthesis rates and mRNA stabilization influence RA along the treatment with Congo Red. Our findings indicate that alterations in synthesis rates primarily drive changes in RA, whereas mRNA stability remains largely unaffected under our conditions, in contrast to other stress responses. Additionally, the RA of RP, RiBi, and ESRup genes is influenced by both mRNA stability and SR, albeit to a lesser extent than in other stress conditions. Moreover, we identified: a) a small subset of genes whose mRNA levels are co-regulated by both changes in synthesis rates and mRNA stability; b) previously unidentified genes whose mRNA levels increase in the presence of Congo Red; and c) RNA-binding proteins (RBPs) such as Nab2 and Hrp1 as potential regulators of genes induced in response to cell wall stress.

overall_design: We quantified the mRNA abundance (RA) and synthesis rate (SR) for all genes of the yeast  over a time course (0, 30, 60, 120, 180, and 240 minutes) of Congo Red treatment (30 µg/ml) using the GRO method (Garcia-Martinez Mol cell 2004; Pérez-Ortín jmb 2013). The SR was derived from the nascent transcription rate (nTR) by normalizing it to the cell volume (no change in samples  t0, t30 & t60: 1x factor, and 1.17, 1.44, 1.65x factors for t120, t180 and t240 samples, respectively).

first: José

last: Pérez-Ortín

last: García-Martínez

first: Raúl

last: García

first: Javier

last: Arroyo


title: Single Cell Minimal Residual Disease Analysis in Multiply Relapsed AML Patient

city: Miami

first: Katarina

last: Micin

state: Florida

address: 1501 NW 10th Ave

institute: University of Miami

type: Genome variation profiling by high throughput sequencing

summary: This patient experienced multiple AML relapses, yet demonstrated exceptional response to the small molecule IDH1 inhibitor Olutasidenib. To further study both the disease and treatment biology specific to this patient, we used a novel single cell AML MRD assay to perform both single cell DNA and protein-level analysis.

overall_design: Cryopreserved Bone Marrow Mononuclear Cells (BMMC) from a multiply relapsed AML patient were CD34 and CD117 enriched, and then underwent single cell DNA and protein sequencing for minimal residual disease (MRD) analysis.


title: BMP, MEK and WNT modulation with NGN2 expression for rapid generation of hiPSC-derived neurons amenable to regional patterning [bulk RNA-seq]

city: Ludwigshafen

first: Peter

last: Reinhardt

address: Knollstrasse

institute: AbbVie Deutschland GmbH & Co. KG

summary: hiPSC are a promising tool for studying neurological diseases and developing therapies for neurodegenerative diseases. Differentiation of hiPSC into neurons can be achieved by dual SMAD inhibition (dSMADi) or induced NGN2 overexpression (“iNGN2”). Starting directly from hiPSC, iNGN2 shortens the time to a neuronal stage but leads to neurons partially resembling peripheral or posterior fates while dSMADi more faithfully recapitulates forebrain development. To modify the iNGN2 paradigm, we applied an accelerated induction paradigm that is dependent on inhibition of BMP, MEK and WNT pathways (“BMWi”), to commit hiPSC into a rostral neuroectoderm fate before iNGN2. The resulting neurons showed strong expression of telencephalic and cortical markers, with decreased levels of peripheral and posterior marker genes compared to iNGN2 alone. The resulting cortical neurons are suitable for a tau aggregation assay. Furthermore, we could demonstrate that during BMWi treatment, the cells are amenable to additional regional patterning cues. This allowed the generation of neurons from different regions of the CNS and PNS, which will significantly facilitate in vitro modeling of a range of neurodevelopmental and neurodegenerative disorders.

overall_design: We performed a comparison of short vs. long differentiation (D14, 21 and 28) of BMWi and dSMAD differentiated neurons in different cell lines (hiPSC_1, hiPSC_3, hiPSC_5 and hiPSC_7). Per experiment 3-4 replicates were generated.

first: Carina

last: Habich

first: Astrid

last: Wachter

first: Juergen

last: Korffman

first: Timo

last: Lange


title: Identification and Correction of Time-Series Transcriptomic Anomalies[K562_timeseries]

city: Durham

first: Steven

last: Haase

state: North Carolina

department: Biology

institute: Duke University

summary: Analysis and visualization of time-series transcriptomic data revealed Sudden TRanscriptomic Irregular Profile Expression changes (STRIPEs), characterized by anomalous transcript level values across the transcriptome in a given time point. We developed quantitative methods for detection and correction of STRIPEs in time-series. Correction of STRIPEs improves the quality of downstream analyses and reproducibility.Here we present cell-cycle transcriptomic time-series experiments containing STRIPEs from two different organisms/experimental conditions: Saccharomyces cerevisiae (BF264-15D background) in YEP 2% Dextrose at 38.5°C (mild chronic heat stress) and the K562 human cell line in RPMI + 10% BCS (bovine calf serum) + P/S.

overall_design: For each time-series cell-cycle experiment, cells were first cell-cycle synchronized using alpha factor mating pheromone or centrifugal elutriation for the S. cerevisiae 38.5°C and the human k562 cell line datasets respectively. Cells were then grown in their respective environmental conditions [Saccharomyces cerevisiae (BF264-15D background) in YEP 2% Dextrose at 38.5°C (mild chronic heat stress) and the K562 human cell line in RPMI + 10% BCS (bovine calf serum) + P/S.] and samples were collected in time-series for RNA sequencing.

first: Sophia

last: Campione

first: Christina

last: Kelliher

first: Cullen

last: Roth

first: Chun-Yi

last: Cho

first: Anastasia

last: Deckard

first: Francis

middle: C

last: Motta


title: SARS-CoV-2 Nsp2 recruits GIGYF2 near viral replication sites and supports viral protein production [nsp2_del_rna_seq]

city: Seoul

first: Sunghan

last: Lee

state: South Korea

address: Building 203 Room 526, 1, Gwanak-ro, Gwanak-gu

department: School of Biological Sciences

institute: Seoul National University

summary: The SARS-CoV-2 genome encodes 16 non-structural proteins (Nsps), with Nsp2 being the least conserved and least understood. In this study, we found a crucial role of Nsp2 in the SARS-CoV-2 life cycle and demonstrated its interaction with GIGYF2, which causes the relocation of GIGYF2 to near double membrane vesicles (DMVs) and the enhancement of viral protein production. Deletion of the Nsp2-coding region from the viral genome led to a drastic reduction in viral RNA synthesis early in infection (3–4 hours post infection). Through interactome analysis of Nsp2 in virus-infected cells, we identified GIGYF2—a protein involved in translational regulation—as a key partner of Nsp2. We confirm the interaction between GIGYF2 and Nsp2 from both SARS-CoV-1 and SARS-CoV-2. Depleting GIGYF2 or its cofactor ZNF598 phenocopied the replication defects observed with Nsp2 deletion, suggesting their critical roles in viral reproduction. Moreover, GIGYF2 and ZNF598 relocate to areas near DMVs, viral replication sites, upon infection. This relocation does not happen with the Nsp2-deleted virus, indicating Nsp2’s role in directing GIGYF2 to DMVs. Using formaldehyde crosslinking and immunoprecipitation-sequencing experiments (fCLIP-seq), we found that GIGYF2 interacts with viral RNAs, particularly in regions encoding Nsp3, M, and Orf6. Depletion of GIGYF2 resulted in decreased expression of these proteins. Our findings reveal the function of Nsp2 in supporting viral protein production by exploiting GIGYF2 as a host factor.

overall_design: We employed formaldehyde immunoprecipitation and sequencing (fCLIP-seq) using anti-GIGYF2 antibody after SARS-CoV-2 infection. To investigate the function of GIGYF2 and NSP2 in SARS-CoV-2 replication, we performed RNA-sequencing after infection with WT and nsp2-deleted virus. We also performed RNA-sequencing in parental and GIGYF2 shRNA cells after SARS-CoV-2 virus infection.


title: SPIDR enables multiplexed mapping of RNA-protein interactions and uncovers a mechanism for selective translational suppression upon cell stress

status: Public on Jun 18 2025

city: New York

first: Marko

last: Jovanovic

state: New York

address: 1212 Amsterdam Avenue

department: Biological Sciences

institute: Columbia University

summary: RNA-binding proteins (RBPs) regulate all stages of the mRNA life cycle, yet current methods generally map RNA targets of RBPs one protein at a time. To overcome this limitation, we developed SPIDR (Split Pool Identification of RBP targets), a highly multiplexed split-pool method that profiles the binding sites of dozens of RBPs simultaneously. SPIDR identifies precise, single-nucleotide binding sites for diverse classes of RBPs. Using SPIDR, we uncovered an interaction between LARP1 and the 18S rRNA and resolved this interaction to the mRNA entry channel of the 40S ribosome using cryo-EM, providing a potential mechanistic explanation for LARP1’s role in translational suppression. We explored changes in RBP binding upon mTOR inhibition and identified that 4EBP1 preferentially associates with translationally repressed mRNAs upon mTOR inhibition. SPIDR has the potential to significantly advance our understanding of RNA biology by enabling rapid, de novo discovery of RNA-protein interactions at an unprecedented scale.

overall_design: A multiplexed eCLIP method to study RNA-binding proteins (RBPs) at scale. Two technical replicates of K562 cells and two experiments with HEK293 cells under control (DMSO) and Torin treatment. Each experiment involves 1 or samples which get sequenced to generate bigwigs for each RBP.

first: Erica

last: Wolin

first: Jimmy

last: Guo

first: Mario

last: Blanco

first: Isabel

middle: N

last: Goronzy

first: Darvesh

last: Gorhe

first: Wenzhao

last: Dong

first: Andrew

middle: A

last: Perez

first: Abdurrahman

last: Keskin

first: Elizabeth

last: Valenzuela

first: Ahmed

last: Abdou

first: Carl

last: Urbinati

first: Ross

last: Kaufhold

first: Tomas

middle: H

last: Rube

first: Jailson

last: Querido

first: Mitchell

last: Guttman


title: BMP, MEK and WNT modulation with NGN2 expression for rapid neuron differentiation from hiPSC amenable to regional patterning [BMWi]

first: Peter

last: Reinhardt

summary: hiPSCs aid in studying neurological diseases and developing therapies. Interventions, such as dual SMAD inhibition or NGN2 overexpression (“iNGN2”), can direct hiPSCs towards neurons. Starting directly from hiPSCs, iNGN2 shortens the time to a neuronal stage but leads to neurons resembling peripheral or posterior fates. We applied an accelerated induction paradigm that is only dependent on inhibition of BMP, MEK and WNT pathways (“BMWi”), to commit iPSCs before to rostral neuroectoderm. The resulting neurons showed strong expression of telencephalic, cortical markers, with decreased levels of peripheral and posterior marker genes compared to iNGN2 alone. The resulting cortical neurons are suitable for a tau aggregation assay. Furthermore, we could demonstrate that during BMWi treatment, the cells are amenable to regional patterning clues. This allowed the generation of neurons from different regions of the CNS and PNS, which will significantly improve existing in vitro models for neurodegenerative disorders.

overall_design: We performed a comparison of iPSCs, iNGN2 and BMWi differentiated neurons at different days of differentiation. Neurons were plated in either NMM+ or NMM- (Neurobasal and B27 with or without retinoids). BMWi cells were replated in NMM- and the medium was changed after 7 days.

first: Carina

last: Habich

first: Astrid

last: Wachter

first: Juergen

last: Korffman

first: Christopher

last: Sliwinski

first: Timo

last: Lange


title: Identifying the role of DNMT1 in gene expression regulation in somatostatinergic interneurons during embryonic corticogenesis [RNA-Seq]

city: Aachen

first: Geraldine

last: Zimmer-Bensch

address: Worringerweg 3

department: Neuroepigenetics

institute: RWTH Aachen University

summary: The establishment of neuronal circuits, made up of excitatory neurons and inhibitory interneurons, is a fine-tuned process during corticogenesis and is pivotal for a functional brain. Developmental aberrations affecting these circuits are implicated in several neuropsychiatric disorders. While excitatory neurons originate in cortical proliferative zones, inhibitory interneurons migrate from the basal telencephalon into the cortex. This migration is regulated by intrinsic genetic programs and extrinsic cues. Here, we aimed to identify the role of the DNA methyltransferase 1 (DNMT1) in controlling the expression of key genes implicated in mouse cortical interneuron development and the migration of somatostatin-expressing interneurons within the developing cortex.

overall_design: FAC-sorted somatostatinergic interneurons from the basal telencephalon were collected from the brains of multiple E14.5 mice, with or without a conditional knockout of Dnmt1 in somatostatinergic interneurons, and pooled per genotype. The samples were sequenced following an RNA extraction and library preparation.

first: Julia

last: Reichard

first: Philip

last: Wolff

first: Chao-Chung

last: Kuo


title: Dissecting the cell autonomous and non-autonomous effects of DNMT1 deletion in cortical somatostatinergic interneurons

summary: The development of cortical circuits, made up of excitatory neurons and inhibitory interneurons, is a fine-tuned and vital process during brain development. Aberrations affecting the establishment of these circuits are implicated in several neuropsychiatric and neurological disorders. While excitatory neurons originate in cortical proliferative zones, inhibitory interneurons migrate from the basal telencephalon into the cortex. This migration is regulated by intrinsic genetic programs and extrinsic cues. Here, we aimed to identify the role of the DNA methyltransferase 1 (DNMT1) in controlling the expression of key genes implicated in the development and migration of post-mitotic somatostatin-positive interneurons as well as its impact on the rest of the cortical population.

overall_design: Medial cortical tissue was dissected from brains of E16.5 mice with or without a conditional knockout of Dnmt1 in somatostatinergic interneurons. The nuclei were extracted via sucrose gradient ultracentrifugation and fixed. Following library preparation based on a split-and-pool approach, the samples were sequenced.

first: Can

last: Yildiz

first: Georg

last: Pitschelatow


title: BMP, MEK and WNT modulation with NGN2 expression for rapid neuron differentiation from hiPSC amenable to regional patterning [BMWi_freeze]

overall_design: We performed a comparison of fresh versus frozen "BMWi" protocol derived neural progenitor cells.


title: MERFISH analysis of Sst-Cre mediated Dnmt1 knockout at E16.5

department: Biology 2

summary:
To investigate the effects of Dnmt1 Knockout in Sst expressing interneurons on celltype distribution in the embryonic brain, Sst-Cre/tdTomato/Dnmt1 loxp2 knockout mice and Sst-Cre/tdTomato control mice were analysed.
10 µm coronal sections of E16.5 brains were prepared for the Merscope platform using the commercially available Pan Neuro panel (Vizgen), covering 500 distinct transcripts.

overall_design: Pilot experiment comparing one knockout with one control section


title: The quantitative impact of 3′UTRs on gene expression

city: Ithaca

first: Andrew

middle: William

last: Grimson

state: NY

address: 526 Campus Rd

department: Molecular Biology and Genetics

institute: Cornell University

type: Non-coding RNA profiling by high throughput sequencing

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

sample_organism:
Escherichia coli
Homo sapiens

platform_organism:
Escherichia coli
Homo sapiens


title: Identification and Correction of Time-Series Transcriptomic Anomalies[Scerevisiae_38_5C_timeseries]

first: Steven

last: Haase

first: Sophia

last: Campione

first: Christina

middle: M

last: Kelliher

first: Cullen

last: Roth

first: Chun-Yi

last: Cho

first: Anastasia

last: Deckard

first: Francis

last: Motta


title: The quantitative impact of 3′UTRs on gene expression [PRO-seq]

summary: Control of gene expression is fundamental to biology, and post transcriptional regulation is an important component of this process. In mammals, the 3′UTR in particular serves as a major source of regulatory information within the transcript. Here, we developed an accurate, high throughput, reporter based system to evaluate the impact of >1,400 full length human 3′UTRs on RNA stability, translational regulation, and total protein output. We used this data to model the relative contributions of RNA stability and translational efficiency towards total 3′UTR mediated regulation, revealing an unexpectedly large role for 3′UTR specified translational control. We observed relationships between GC content and 3′UTR length and different modes of regulation, and identified candidate RNA binding proteins involved in 3′UTR dependent gene expression. We compared regulation from >1,400 3′UTRs under control of two dissimilar promoters, which revealed promoter driven differences in post transcriptional regulation for certain 3′UTRs. Together, this dataset represents a comprehensive characterization of 3′UTR mediated quantitative regulation.

overall_design: Nascent RNA profiling (PRO-seq) of monoclonal landing pad cell lines containing either the PGK or CAG promoter, to measure transcriptome-wide RNA stability (used in combination with RNA-seq performed in parallel)

first: Jessica

middle: D

last: West


title: DNA methylation in PBMC during SIVmac infection in the rhesus macaque

city: Pittsburgh

first: Anna

last: Jasinska

state: PA

address: 3550 Terrace Street

department: School of Medicine

institute: University of Pittsburgh

summary:
We characterized DNA methylation profiles in blood PBMCs across lentiviral infection in a progressing non-human primate model of AIDS - SIVmac infection in the rhesus macaque.
We contrasted methylation data across the course of the SIVmac infection in the young adult and old adult rhesus macaques to identify potential age-related differential methylation patterns and epigenetic clock acceleration.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: DNA methylation profiles were generated from 40 PBMC samples from 5 old adults and 5 young adults at 4 time points from the baseline across acute infection, early and late chronic infection. For DNA methylation analysis, we utilized custom Infinium methylation array HorvathMammalMethylChip40.

first: Ivona

middle: V

last: Pandrea

first: Cristian

last: Apetrei


title: Truncated NTRK2 is induced in CAP1 endothelial cells during mouse lung injury-repair

first: Jichao

last: Chen


title: The quantitative impact of 3′UTRs on gene expression [miRNA-seq]

overall_design: Small RNA-sequencing of monoclonal landing pad cell lines containing either the PGK or CAG promoter to identify differentially expressed miRNAs


title: The quantitative impact of 3′UTRs on gene expression [plasmid-seq]

overall_design: Plasmid DNA sequencing to identify barcodes linked to 3′UTR reporters, performed by tagmentation library prep (with Tn5 transposase)


title: The quantitative impact of 3′UTRs on gene expression [amplicon-seq]

overall_design: Measuring protein output, translational efficiency, and RNA stability for library of >1,400 GFP 3′UTR reporters under control of two different promoters. Reporters are quantified with amplicon sequencing, targeted to barcodes identifying each 3′UTR.


title: BMP, MEK and WNT modulation with NGN2 expression for rapid neuron differentiation from hiPSC amenable to regional patterning

first: Peter

last: Reinhardt

overall_design: Refer to individual Series


title: Screening and Validation of Key Genes Involved in Castration-Resistant Prostate Cancer Based on Transcriptomics Sequencing

status: Public on Jun 17 2025

city: Dalian

first: Wang

last: Yang

address: 9 Lvshun South Rd West Section, Lüshunkou District, Dalian, Liaoning, China

department: Institute of Cancer Stem Cell

institute: Dalian Medical University

summary: Rationale: Prostate cancer is one of the most common malignant tumors occurring in the male reproductive system. Androgen deprivation therapy (ADT) is the primary treatment for prostate cancer. However, approximately 10% to 20% of advanced prostate cancer patients progress to castration-resistant prostate cancer (CRPC) within five years, posing a significant challenge to treatment. There is an urgent need to explore the causes and mechanisms of prostate cancer progression, and to identify new therapeutic targets and predictive markers.Methods: Utilize RNA-seq to screen for differentially expressed genes and alternative splicing events between androgen-sensitive prostate cancer cells and castration-resistant prostate cancer cells. Perform bioinformatics analysis on the differentially expressed genes. The expression levels of these genes were confirmed by real-time quantitative PCR (RT-qPCR); alternative splicing events related to castration resistance were verified through RT-PCR. The impact of the S100A6 gene on the proliferation and growth capabilities of PC3 and DU145 cells was analyzed using CCK8, colony formation, and EdU assays. Cell migration was assessed using a wound healing assay.Results: The RNA-seq analysis results showed that there were 4,830 differentially expressed genes in non-hormone-sensitive prostate cancer. GO and KEGG enrichment analysis of these differentially expressed genes revealed significant enrichment in tumor-related signaling pathways such as regulation of cell cycle process, cell division, and regulation of cell projection organization. Further RT-qPCR detection results indicated that the mRNA expression of four genes, including S100A6, was upregulated, consistent with the transcriptome sequencing results. Downregulation of S100A6 expression significantly inhibited the proliferation and migration of non-hormone-dependent prostate cancer. In this study, we also identified many splicing alterations in cancer-related genes, with castration resistance-induced alternative splicing events closely related to the interaction networks of regulation of cell cycle process, cell division, and regulation of cell projection organization.Conclusions: Our research findings suggest that S100A6 may serve as a molecular marker or therapeutic target associated with castration resistance in prostate cancer, providing new insights into the molecular basis of this disease.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for LNCAP cells (ADPC) and PC3, DU145 cells (CRPC).

first: Guangquan

last: Tong

first: Xiaomeng

last: Jing

first: Wenjing

last: Zhang

first: Yuesheng

last: Lv


title: Determination of Trunk Neural Crest Cell Fate and Susceptibility to Splicing Perturbation by the DLC1-SF3B1-PHF5A splicing complex

city: Hong Kong

first: Jingkai

last: Wang

address: The University of Hong Kong, Pokfulam

institute: University of Hong Kong

summary: How the ubiquitously expressed splicing factors specifically regulate neural crest (NC) development and enhance their vulnerability to splicing perturbations remain poorly understood. Here, we show that NC-specific DLC1, partnering with SF3B1-PHF5A splicing complex, are crucial for determining avian trunk NC cell fate by regulating the splicing of NC specifiers SOX9 and SNAI2 pre-mRNAs rather than their upstream regulators BMP4, WNT1, and PAX7. Mechanistically, SF3B1-PHF5A binds to the intronic branch site (BS) sequences of all factors, while DLC1 interacts with a specific motif near the BS sequences of SOX9 and SNAI2, thereby determining their functional specificity in NC specification. Moreover, DLC1 increases NC cells’ vulnerability to splicing modulator pladienolide B by reducing the binding capacity of the SF3B1-PHF5A splicing complex to the shorter length of both SOX9 intron 2 and SNAI2 intron 1, which possess weaker polypyrimidine tract 3’ of the BS sequence, resulting in intron retention and loss of NC progenitors. Conversely, somite specific SLU7-SF3B1-PHF5A splicing complex regulates SOX9 and SNAI2 expression and imparts resistance to PB. Our data reveal the cell-type specific splicing complexes with distinct vulnerabilities to PB, highlighting the critical role of the DLC1-SF3B1-PHF5A in determining trunk NC cell fate and enhancing its susceptibility to splicing perturbation.

overall_design: RNA-seq profiling of GFP+ cells following CRISPR-Cas9-mediated knockout of DLC1, PHF5A, and SF3B1 compared to scrambled gRNA control samples.

first: Zhengfan

last: Zheng

first: Suisui

last: Guo

first: Hoi-Yau

last: Tam

first: Yanxia

last: Rao

first: Man-Ning

last: Hui

first: May

middle: P

last: Cheung

first: Alan

middle: W

last: Leung

first: Kelvin

middle: K

last: Wong

first: Rakesh

last: Sharma

last: Liu

first: Martin


title: SLAMF1 is regulated by macrophage-CD4 T cell contact and confers protection to Mycobacterium tuberculosis

city: St. Louis

first: Jennifer

last: Philips

state: Missouri

address: 660 S Euclid Avenue

department: Department of Medicine

institute: Washington University in St.louis

summary: CD4 T cells are crucial for protective immunity to Mycobacterium tuberculosis (Mtb). Because CD4 T cell protection depends upon direct interaction with infected macrophages, we sought to identify contact-dependent protective factors. We discovered that direct contact with antigen-specific CD4 T cells drives signaling lymphocytic activation molecule family member 1 (SLAMF1/CD150) expression on macrophages. SLAMF1 is a cell-surface receptor that mediates homotypic interactions between hematopoietic cells, interacts with microbes, and promotes macrophage antimicrobial responses. In mice, SLAMF1 expression was induced on Mtb-infected myeloid cells in a T cell-dependent manner and partially impaired in autophagy-deficient macrophages. In non-human primates, antigen presentation by lung macrophages induced SLAMF1 expression in a manner that correlated with T cell abundance and vaccine protection. Finally, in mice SLAMF1 limited Mtb burden and inflammatory responses during Mtb infection. We conclude that SLAMF1 is a T cell contact-dependent factor in macrophages that contributes to host protection from TB.

overall_design: IFNγ-treated Bone marrow derived macrophages (BMDMs) were infected with mCherry-expressing Mycobacterium tuberculosis (H37Rv Strain) at a multiplicity of infection (MOI) of 1. Three hours post infection, antigen-specific Nur77-GFP P25TCR-Tg effector T cells were added to the macrophages at a ratio of 1:1. Twenty four hours later the cells were harvested and stained with fluorescent conjugated antibodies against selected surface markers and were sorted by flow cytometry. CD11b+ BMDMs were sorted into infected and bystander cells according to mCherry Fluorescence. Antigen-specific P25TCR-tg T cells were sorted based on CD4 Surface expresssion. RNA was extracted from sorted cells and bulk RNA sequencing was performed

first: G

last: Prasad

first: Steven

middle: J

last: Grigsby

first: Gideon

last: Erkenswick

first: Cynthia

last: Celhay

first: Ekansh

last: Mittal

first: Guozhe

first: Samuel

last: Fallon

first: Thais

last: Klevorn

first: Neharika

last: Jain

first: Makedonka

last: Mitreva

first: Amanda

last: Martinot

first: Joel

last: Ernst


title: The Nrf2-HMOX1 pathway as a therapeutic target for reversing cisplatin resistance in non-small cell lung cancer via ferroptosis inhibition

city: Nantong,Jiangsu,China

first: Lili

last: Ji

state: 江苏省

address: No. 19 Qixiu Road, Nantong University, Chongchuan District, Nantong City, Jiangsu Province

institute: Nantong University

summary: Cisplatin resistance is a major cause of poor prognosis in non-small cell lung cancer (NSCLC). Cisplatin-induced lung cancer cell death is associated with ferroptosis, a type of recently identified programmed cell death. Nrf2 is a critical component of the antioxidant system, and its pro-tumorigenic activity in lung cancer has been extensively studied. However, the role of Nrf2 in cisplatin-induced ferroptosis and drug resistance remains elusive. Here, we demonstrate that cisplatin treatment induced ferroptosis in parental A549 lung adenocarcinoma cells, and that this effect was significantly reduced in cisplatin-resistant A549/DDP cells. Knocking down Nrf2 sensitized A549/DDP cells to cisplatin-induced cytotoxicity by enhancing ferroptosis. Moreover, we demonstrated that Nrf2 promotes the expression of HMOX1, and the Nrf2-HMOX1 pathway is critical in mediating the anti-ferroptotic function. Additionally, immunohistochemical analysis of NSCLC specimens indicated that the Nrf2 expression was correlated with HMOX1, and high levels of Nrf2 and HMOX1 were associated with poor patient survival. These findings suggest that the HMOX1-Nrf2 pathway significantly influences treatment outcomes in NSCLC. Ultimately, we demonstrated that treatment with Nrf2 inhibitor ML385 promoted ferroptosis by inhibiting the Nrf2-HMOX1 pathway, restoring cisplatin sensitivity in drug-resistant cells. Our findings provide insights into the mechanism underlying cisplatin resistance and suggests that targeting the Nrf2-HMOX1 pathway enhances cisplatin-induced ferroptosis and improves NSCLC treatment outcomes.

overall_design: RNA-seq profiling of A549/DDP cells and their knockdown derivatives (shNrf2)

first: Xiaorong

last: Zhou

first: Xinru

last: Zou

first: Ling

last: Zuo

first: Shuning

last: Hu

first: Yixuan

last: Fang


title: Tissue DNA methylation during SIVmac infection in the rhesus macaque

first: Anna

last: Jasinska

type: Methylation profiling by genome tiling array

summary:
We characterized DNA methylation profiles across lentiviral infection in a progressing non-human primate model of AIDS - SIVmac infection in the rhesus macaque.
We contrasted methylation data across the course of the SIVmac infection in the young adult and old adult rhesus macaques to identify potential age-related differential methylation patterns and epigenetic clock acceleration.

overall_design: DNA methylation profiles were generated from 56 tissue samples from 6 solid tissues (cerebellum, transverse colon, liver, heart, spleen, and peritoneal fat) from 6 old adults and 4 young adults. For DNA methylation analysis, we used a custom Infinium methylation array HorvathMammalMethylChip40.

first: Ivona

last: Pandrea

first: Cristian

last: Apetrei


title: Assessing the role of FcγRIIIa expression on CD8 T cells

first: Stylianos

last: Bournazos

address: 1230 York Ave

institute: The Rockefeller University

summary: Fcγ receptors (FcγRs) are ubiquitously expressed by nearly all lineages of innate and adaptive leukocyte populations, with the notable exception of T cells, which are negative for all classes of FcγRs. While at steady state T cells are negative for all FcγR classes, we observed that a subset of CD8 T cells specifically induces the expression of the activating FcγR, FcγRIIIa, in response to viral infection. We used scRNAseq to compare the transcriptional profile of FcγRIIIa+ and FcγRIIIa- CD8 T cell populations from the lungs of influenza-infected FcγR humanized mice.

overall_design: Cells (NK cells and T cells) from the lungs of influenza-infected FcγR humanized mice were isolated by FACS and analyzed by scRNAseq to determine the gene expression profile and T-cell receptor repertoire.

first: Kevin

last: Kao

first: Jeffrey

last: Ravetch


title: Identification of DNMT1-interacting chromatin and its dynamic properties [ChIP-Seq]

first: Geraldine

last: Zimmer-Bensch

summary: Epigenetic mechanisms are dynamic processes that govern gene expression in health and disease. DNA methylation, catalyzed by DNA methyltransferases (DNMTs) such as DNMT1, represents a stable but reversible process in which DNA is chemically modified to facilitate or prevent the binding of transcriptional regulators. Despite being a vital component of transcriptional regulation throughout all stages of life in health and disease, the sequence specificity of DNMT-binding is so far poorly understood. Here, we aimed to identify potential binding sites of DNMT1 as well as the dynamics of this process in immortalized, murine cerebellar granule cells, with and without the presence of a recombinant ephrinA5 protein, a ligand known to play a crucial role in neurodevelopment.

overall_design: Chromatin immunoprecipitation sequencing for DNMT1 in immortalized cerebellar granule cells treated with Fc control or recombinant ephrinA5-Fc. Inputs were equimolarly pooled per treatment.

first: Can

middle: B

last: Yildiz

first: Mira

last: Jakovcevski

first: Chao-Chung

last: Kuo


title: BMP, MEK and WNT modulation with NGN2 expression for rapid generation of hiPSC-derived neurons amenable to regional patterning [snRNA-seq]

first: Peter

last: Reinhardt

summary: hiPSC are a promising tool for studying neurological diseases and developing therapies for neurodegenerative diseases. Differentiation of hiPSC into neurons can be achieved by dual SMAD inhibition (dSMADi) or induced NGN2 overexpression (“iNGN2”). Starting directly from hiPSC, iNGN2 shortens the time to a neuronal stage but leads to neurons partially resembling peripheral or posterior fates while dSMADi more faithfully recapitulates forebrain development. To modify the iNGN2 paradigm, we applied an accelerated induction paradigm that is dependent on inhibition of BMP, MEK and WNT pathways (“BMWi”), to commit hiPSC into a rostral neuroectoderm fate before iNGN2. The resulting neurons showed strong expression of telencephalic and cortical markers, with decreased levels of peripheral and posterior marker genes compared to iNGN2 alone. The resulting cortical neurons are suitable for a tau aggregation assay. Furthermore, we could demonstrate that during BMWi treatment, the cells are amenable to additional regional patterning cues. This allowed the generation of neurons from different regions of the CNS and PNS, which will significantly facilitate in vitro modeling of a range of neurodevelopmental and neurodegenerative disorders.

overall_design: The aim of this study was to observe the progression of BMWi differentiation (hiPSC, day 6 of the protocol and final neurons) using snRNA sequencing and thus to examine the heterogeneity of the culture. For comparison, iNGN2 neurons were also examined.

first: Carina

last: Habich

first: Michael

last: Wolf

first: Markus

last: Kummer

first: Astrid

last: Wachter


title: Identifying the role of DNMT1 on methylation signatures in somatostatinergic interneurons during embryonic corticogenesis [EM-seq]

type: Methylation profiling by high throughput sequencing

summary: The establishment of neuronal circuits, made up of excitatory neurons and inhibitory interneurons, is an intricately regulated process during development and is vital for proper brain function. Its perturbations are increasingly implicated in several neuropsychiatric disorders. While excitatory neurons are born in proliferative zones of the cortex, cortical inhibitory interneurons are born in the basal telencephalon and migrate into the cortex. This process is regulated by intrinsic genetic programs as well as extrinsic cues. Here, we aimed to characterize the role of the DNA methyltransferase 1 (DNMT1) in controlling the methylation of key genes implicated in the development and the migration of somatostatin-expressing interneurons within the developing murine cortex.

overall_design: FAC-sorted somatostatinergic interneurons from the basal telencephalon were collected from the brains of multiple E14.5 mice, with or without a conditional knockout of Dnmt1 in somatostatinergic interneurons, and pooled per genotype. The samples were sequenced following a DNA extraction and library preparation.

first: Julia

last: Reichard

first: Philip

last: Wolff


title: Single cell RNA sequencing on synovium, meniscus and cartilage of rheumatoid arthritis

city: Guangzhou

first: Xiaobin

last: Lin

state: Guangdong

address: 107 Yanjiang West Road, Yuexiu District, Guangzhou City, Guangdong Province

department: Department of Joint Surgury

institute: Sun Yat-sen Memorial Hospital, Sun Yat-sen University

summary: Rheumatoid arthritis (RA) induced destruction of knee joints is a common cause of total knee arthroplasty (TKA). Under single cell RNA sequencing generated by 10x Genomics, we identified CD142+ synovial fibroblasts as a novel cluster, located at the sublining layer in normal and osteoarthritis knee synovium, but elevated and distributed at the lining layer in RA knee synovium, and infiltrated in multiple RA joint synovia. Intra-articular injection of CD142+ synovial fibroblasts can quickly and drastically damage the meniscus but has a slight effect on cartilage.Long-term follow-up of the RA cohort indicated that enriched CD142+ synovial fibroblasts in the lining layer was a risk factor for severe joint destruction and eventually underwent TKA. Our results demonstrate that CD142+ synovial fibroblasts can be used as an indicator to assess prognosis and a therapeutic target to inhibit meniscal damage, thereby alleviating RA knee joint destruction.

overall_design: This dataset presents scRNA-seq raw and processed data files on RA cartilage, meniscus, and synovium. Fresh human cartilage, meniscus and synovial tissues obtained from the same RA knee by total knee arthroplasty were made into cell suspensions, and were captured with 10x Genomics based on the NovaSeq 6000 platform. For tsv.gz file, it is original processed matrix file. For RDS file, it is Seurat file that contains celltype reference.

first: Hao

last: Sun

first: Fangzhou

last: Liu

first: Yingbin

last: Zhang

first: Jianda

last: Ma

first: Zhencheng

last: Huang

first: Junming

first: Lutian

last: Yao

first: Mengyuan

first: Meiyi

last: Chen

first: Jie

last: Xu

first: Yulong

last: Wei

first: Lie

last: Dai

first: Ruofan


title: Protein sequence editing defines distinct and overlapping functions of SKN-1A/Nrf1 and SKN-1C/Nrf2.

city: Seattle

first: Nicolas

last: Lehrbach

state: WA

address: 1100 Fairview Ave. N, Seattle, WA 98109-102.

institute: Fred Hutchinson Cancer Center

summary: Nrf/NFE2L family transcription factors regulate redox balance, metabolism, proteostasis, and aging. Nrf1/NFE2L1 is responsible for stress-responsive upregulation of proteasome subunit genes and is essential for adaptation to proteotoxic stress. The closely related Nrf2/NFE2L2 is responsible for activation of oxidative stress responses and xenobiotic detoxification. Although regulated by different mechanisms, Nrf1 and Nrf2 contain very similar DNA binding domains and can drive similar transcriptional responses. However, the extent to which functions of Nrf1/2 are distinct or overlapping has been unclear. In C. elegans, a single gene, skn-1, encodes distinct protein isoforms, SKN-1A and SKN-1C, that function analogously to mammalian Nrf1 and Nrf2, respectively. We previously showed that regulation of the proteasome by SKN-1A/Nrf1 requires post-translational conversion of N-glycosylated asparagine residues to aspartate by the PNG-1/NGLY1 peptide:N-glycanase, a process we term ‘sequence editing’. Here, we reveal the consequences of sequence editing for the transcriptomic output of activated SKN-1A. We show that whilst activation of proteasome subunit genes is strictly dependent on sequence editing, sequence edited SKN-1A also activate genes linked to redox homeostasis and xenobiotic detoxification that are also activated by non-sequence edited forms of SKN-1. Using mutant alleles that selectively inactivate either SKN-1A or SKN-1C, we show that SKN-1A/Nrf1 and SKN-1C/Nrf2 function coordinately to promote optimal oxidative stress resistance and confirm that they are regulated by discrete genetic pathways. This work demonstrates that sequence editing plays a critical role in tailoring SKN-1/Nrf functions by tuning the SKN-1A/Nrf1 regulated transcriptome.

overall_design: We used RNAseq to compare gene expression in animals expressing trunacted forms of the SKN-1 transcription factor that are altered with different patterns of Asn to Asp substitutions. For each transgenic strain, we compared gene expression to stage-matched wild type (non-transgenic) control samples. Samples were prepared from synchronized L4 stage animals. We analyzed four replicate samples for each of three transgenic strains (GR3105, NJL2494, NJL2492) and four replicate samples of the wild type control strain (N2).

first: Briar

last: Jochim

first: Irini

last: Topalidou


title: Catalytic inhibition of KAT6 /KAT7 enhances the efficacy and overcomes primary and acquired resistance to Menin inhibitors in MLL leukaemia [RNA-seq]

city: Melbourne

first: Mark

last: Dawson

address: 305 Grattan Street

institute: Peter MacCallum Cancer Centre

summary: Understanding the molecular pathogenesis of MLL leukaemia has led to the development of epigenetic therapies that have altered the natural history of this often-incurable disease. Here, using complementary genetic and pharmacological approaches, we define the individual and combined contribution of the MYST acetyltransferases, KAT6A, KAT6B and KAT7, to MLL fusion oncoprotein (MLL-FP) driven acute leukaemia. We show that inhibition of KAT6A/B is efficacious in some but not all MLL-FP pre-clinical models; however, simultaneous targeting of KAT7 increases the therapeutic effect. At a molecular level, KAT7 interacts with Menin and other members the MLL complex and we demonstrate that these epigenetic regulators are co-localised at chromatin where they co-regulate the oncogenic transcriptional program initiated and maintained by the MLL-FP. Catalytic inhibition of KAT6/KAT7 with the novel small molecule inhibitor PF-9363 provides an orthogonal route to Menin inhibition to disable the transcriptional activity of MLL-FP. This is of clinical importance as PF-9363 or genetic depletion of KAT7 is able to overcome both genetic and non-genetic acquired resistance to Menin inhibition. Moreover, combined inhibition of KAT6/KAT7 and Menin results in a rapid eviction of chromatin bound MLL-FP and a profound repression of the oncogenic transcriptional program resulting in marked synergistic benefit in pre-clinical models of primary resistance to single agent therapy. Together these data provide the molecular rationale for rapid clinical translation of combination therapy to further improve clinical outcomes in MLL-FP leukaemia.

overall_design: To investigate the effects of KAT6/KAT7 and menin inhibition in MLL-FP leukaemia, RNA-Seq was performed on cells treated for 6 and 24 hours in 3 biological replicates for transcriptomic analysis.

first: Shellaina

last: Gordon


title: Effect of stable genetic ablation and pharmacological inhibition of SMYD3 on gene expression in CRC cell line (HCT-116)

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

country: Italy

institute: IRCSS Istituto Nazionale Tumori

summary: Cancer stem cells (CSC) are responsible for colorectal cancer (CRC) chemoresistance, recurrence, and metastasis. Therefore, it has become crucial finding critical molecular stemness targets that are essential for tumor growth. Here, we performed an extensive in vitro and in vivo molecular and functional characterization revealing the pivotal role of SMYD3 in CSC biology. Specifically, SMYD3 interacts with and methylates c-MYC at K158 and K163, modulating its transcriptional activity implicated in stemness and colorectal malignancy. Together, all the in vitro data collected, suggest that SMYD3 pharmacological inhibition affects clonogenic and self-renewal potential of patient-derived CRC-SCs and organoids by altering their molecular signature. Moreover, we showed that SMYD3 stable knock-out or its pharmacological inhibition drastically reduced CRC tumorigenicity in vivo, and reduced the metastatic potential of CRC-SCs. Thus, our findings identify SMYD3 as a promising therapeutic target, acting directly on c-MYC, with potential implications for countering CRC-SCs proliferation, chemoresistance, and metastatic dissemination.

overall_design: To investigate the function of SMYD3 in the regulation of stemness molecular signature, we established HCT-116 SMYD3-KO cell line by CRISPR/Cas9 genome editing. Moreover, we obtained the pharmacological inhibition of SMYD3 by the administration of EM127 the covalent SMYD3 inhibitor. We then performed gene expression profiling analysis using data obtained from RNA-seq of HCT-116 parental, HCT-116 SMYD3-KO and HCT-116 treated with EM127 for 24 hours. We performed a comparative gene expression profiling analysis of RNA-seq data for HCT-116 treated or not with EM127, and parental vs SMYD3-KO.

first: Vittoria

last: Disciglio


title: Effects of alcohol on the transcriptome, methylome, and metabolome of in vitro gastrulating human embryonic cells

status: Public on Jun 16 2025

city: Helsinki

first: Nina

last: Kaminen-Ahola

address: Haartmaninkatu 8

department: Department of Medical and Clinical Genetics

country: Finland

institute: University of Helsinki

summary: Prenatal alcohol exposure (PAE) affects embryonic development, causing a variable fetal alcohol spectrum disorder (FASD) phenotype with neurodevelopmental disorders and birth defects. To explore the effects of PAE on gastrulation, we used an in vitro model with subchronic moderate (20 mM) and severe (70 mM) ethanol exposures during the differentiation of human embryonic stem cells into germ layer cells. We analysed genome-wide gene expression (mRNA sequencing), DNA methylation (EPIC Illumina microarrays), and metabolome (non-targeted LC-MS) of the endodermal, mesodermal, and ectodermal cells. The largest number of ethanol-induced alterations were observed in endodermal cells, whereas the most prominent changes were in ectodermal cells. Methionine metabolism and genes of the major signaling pathways involved in gastrulation and body patterning were affected by ethanol in all germ layers. Many of the altered genes, including BMP4, FGF8, SIX3, and LHX2, have previously been associated with PAE and phenotypes of FASD, like defects in heart and corpus callosum development as well as holoprosencephaly. Our findings support the early origin of alcohol-induced developmental disorders and strengthen the role of methionine cycle in the etiology of FASD.

overall_design: We performed 3’mRNA-sequencing (mRNA-seq) for controls as well as 20 mM and 70 mM EtOH-exposed cells of human embryonic germ layers.

first: Essi

last: Wallén

first: Karita

last: Rämö

first: Jussi

last: Vehviläinen

first: Joonas

last: Sokka

first: Marko

last: Lehtonen

first: Timo

last: Otonkoski

first: Ras

last: Trokovic

first: Pauliina

last: Auvinen

first: Olli

last: Kärkkäinen


title: Effects of alcohol on the transcriptome, methylome, and metabolome of in vitro gastrulating human embryonic cells [array]

overall_design: We used DNAm microarrays (Infinium MethylationEPIC BeadChip v1 and v2, Illumina) to explore the effects of 20 mM and 70 mM EtOH on the genome-wide DNAm of germ layer cells.


title: The quantitative impact of 3′UTRs on gene expression [RNA-seq]

first: Andrew

last: Grimson

overall_design: Gene expression profiling of monoclonal landing pad cell lines containing either the PGK or CAG promoter

first: Jessica

last: West


title: In-depth examination of an iPSC-derived model of human eye development identifies multiple embryonic cell types of critical importance to ocular genesis and disease

city: Milwaukee

first: Xiaolong

last: Ma

state: Wisconsin

address: 8701 W Watertown Plank Rd

institute: Medical College of Wisconsin

summary: Human ocular cell cultures commonly used for disease modeling recapitulate later stages of specialized tissue differentiation, requiring the development of new models to test genetic variants affecting earlier embryonic time points. Here we provide an in-depth characterization of a recently presented 2D model mimicking whole eye development derived from human iPSCs, known as SEAMs. Our study focused on evaluating both morphological and transcriptomic changes occurring at several time points as SEAMs formed over the course of a 28-day differentiation process, with an emphasis on an intermediate stage (Day 14) and a late stage (Day 28) of SEAM development. Transcriptomic profiling using bulk and single cell RNA sequencing was followed by clustering/annotation, pathway enrichment, ligand-receptor interaction, and differentiation trajectory analyses. Bulk RNA sequencing identified 7 major expression trends and their drivers across all time points. Single cell analyses revealed 12 and 14 partially overlapping, yet distinct clusters at Day 14 and 28, respectively, showing a progression from less (optic cup and anterior segment precursors) to more (mature retina, retinal pigmented epithelium, lens, and cornea, including limbal epithelial stem cells) differentiated cell types based on characteristic transcriptional signatures, corroborated by pseudotime and RNA velocity analyses. Establishment of a temporal baseline of SEAM development enables future investigations into how disease-causing variants may disrupt the early stages of human eye development leading to complex ocular phenotypes.

overall_design: SEAM cultures were processed for transcriptomic profiling at Day 0 (reference), 14 and 28 using bulk (2 biological replicates) and single cell (1 biological replicate) RNA sequencing.

first: Maria

middle: R

last: Replogle

first: Chien-Wei

last: Lin

first: Elena

last: Semina


title: The histone H3 lysine 36 demethylase KDM2A/FBXL11 is essential for germ cell development in male mice [ChIP-Seq]

city: Basel

first: Antoine

last: Peters

address: Maulbeerstrasse 66

institute: Friedrich Miescher Institute

summary: KDM2A/FBXL11 is a Jumonji-domain containing lysine demethylase catalyzing the removal of mono- and di-methyl modifications of histone H3 lysine 36. While Kdm2a is required for mouse embryogenesis, its role in adult physiology is unknown. Using conditional deletion approaches, we demonstrate that Kdm2a deficiency causes testicular atrophy and male infertility. Though spermatogonial stem cells were unaffected, proliferating and differentiating spermatogonia suffered from delayed cell cycle progression and apoptosis, which correlated with upregulated expression of several cell cycle inhibitors. Loss of Kdm2a in spermatocytes disrupted progression through meiotic prophase, as shown by impaired chromosome synapsis and  processing  of  meiotic  double  strand  breaks,  and  by  altered  chromatin  states.  Correspondingly, Kdm2a mutant spermatocytes failed to activate numerous genes controlling these processes. RNA-sequencing analyses on purified spermatogonia and spermatocytes showed that during normal spermatogonial differentiation over 700 genes undergo repression, which is controlled by KDM2A. CpG-rich promoter genes upregulated in Kdm2a deficient cells are marked by Polycomb Repressive Complexes (PRC) and associated modifications in wildtype male germ cells, suggesting that KDM2A is required for PRC-mediated repression. Our study thus identifies critical roles for KDM2A in coordinating gene expression programs during spermatogonial differentiation and meiosis, which are essential for male germ cell development.

overall_design: Chromatin profiling analysis using data obtained from anti-H3K4me3 , anti-H3K27me3 and anti-H3K36me2 ChIP from chromatin prepared from FACS sorted populations enriched for Differentiated Spermatogonia (SgD) from ctr and iKO mice

first: Grigorios

last: Fanourgakis


title: Cancer cell type-specific derepression of transposable elements by inhibition of chromatin modifier enzymes

first: Divyesh

last: Patel

address: University of Helsinki

department: Applied Tumor Genomics Program, Research Programs Unit, Faculty of Medicine,

summary: Derepression of transposable elements (TE) by epigenetic therapy leads to the activation of immune response in cancer cells. However, the molecular mechanism of TE regulation by distinct chromatin modifier enzymes (CME) in context of p53 is still elusive. Here, we used FDA-approved epigenetic drugs to systematically inhibit distinct CMEs in p53 wild-type and p53-mutant colorectal, esophageal, and prostate cancer cells. We show that distinct TE subfamilies are derepressed by inhibition of different CMEs in cell type-specific manner. Co-inhibition of DNMT and HDAC (DNMTi-HDACi) had the most consistent effect across cancer types. Loss of p53 results in stronger TE activation and TE-chimeric transcript expression and this effect is largely mediated by the non-genomic actions of p53. Robust immune response elicited by DNMTi-HDACi is due to induced inverted repeat Alu expression concomitant with reduced ADAR1-mediated Alu RNA editing. Collectively, our systematic analyses provide insights for rational use of epigenetic therapies in distinct cancers.

overall_design: Refer to individual Series

first: Ville

last: Tiusanen

first: Konsta

last: Karttunen

first: Päivi

last: Pihlajamaa

first: Biswajyoti

last: Sahu


title: The invasion phenotypes of glioblastoma depend on plastic and reprogrammable cell states

status: Public on Jun 15 2025

city: Uppsala

first: Ida

last: Larsson

address: Dag Hammarskjölds Väg 20

country: Sweden

institute: Uppsala University

summary: Glioblastoma (GBM), the most common primary brain cancer in adults, is characterized by rapid local invasion along diverse routes, such as infiltration of white matter tracts and penetration of perivascular spaces. We investigate the hypothesis that GBM invasion routes correlate with the transcriptional states of individual cells and identify regulators of route-specific invasion. Utilizing patient-derived GBM xenograft models, we integrate single-cell transcriptomics and spatial proteomics, revealing that mesenchymal and oligodendrocyte progenitor-like GBM cells migrate perivascularly, while neural progenitor and astrocyte-like GBM cells invade diffusely. Computational reconstruction identifies ANXA1 as a perivascular invasion driver and lineage-restricted transcription factors RFX4 and HOPX as drivers of diffuse invasion, predictive of patient survival. Genetic ablation of these genes alters invasion phenotypes and extends survival in xenografted mice, clarifying the role of cell states in GBM invasion, and highlighting potential therapeutic targets for selective invasion route targeting in GBM patients.

overall_design: Patient-derived GBM cells and cells from patient-derived GBM xenografts were isolated and analyzed using scRNA-seq. Additionally, generated knock-out (KO) PDC/PDX cells were isolated and analyzed using scRNA-seq.

first: Milena

last: Doroszko

first: Rebecka

last: Stockgard

first: Irem

last: Yildirim

first: Sven

last: Nelander


title: Dietary fermentable polyols fuel gut inflammation through M1 macrophage polarization and gut microbiota

status: Public on Jun 14 2025

city: Minato ku

first: Yun-Gi

last: Kim

institute: Kitasato University

summary: While fermentable oligo- and di-, mono-saccharides and polyols (FODMAPs) have been implicated in exacerbating inflammatory bowel disease (IBD) symptoms, the exact influence of FODMAPs on gut microbiota and inflammation is unclear. Here, we show that sorbitol, a polyol, exacerbates colitis in mice induced by dextran sodium sulfate (DSS). Sorbitol increases the expression of inflammatory genes including Il1b in the colon, associated with M1 macrophage-related genes elevated in IBD patients. Indeed, sorbitol treatment leads to a higher proportion of M1 macrophages in the colon, worsening colitis, which is reversed in IL-1β-deficient mice and mitigated with antibiotic treatment. Sorbitol alters the composition of gut microbiota and metabolites, with Prevotellaceae and tryptamine positively correlated with colonic M1 macrophages. Tryptamine stimulation enhances M1 macrophage polarization. Taken together, polyol consumption activates intestinal macrophages by altering the gut microbiome, which in turn promotes intestinal inflammation.

overall_design: Mice in the sorbitol group were given a solution containing 5% (w/v) sorbitol (FUJIFILM Wako Pure Chemical Corporation) for two weeks.

first: Kensuke

last: Sato

first: Miwa

last: Tomioka


title: The histone H3 lysine 36 demethylase KDM2A/FBXL11 is essential for germ cell development in male mice [RRBS]

overall_design: DNA methylation profiling analysis using data obtained from RRBS from DNA extracted from FACS sorted populations enriched for Differentiated Spermatogonia (SgD) from ctr mice and iKO mice