title: Upregulated cholesterol biosynthesis facilitates the survival of methylation-retaining AML cells following decitabine treatment. [scTEM-Seq]

summary: DNA hypomethylating agents (HMAs) are used to treat acute myeloid leukaemia (AML) and myelodysplasia patients who are unsuitable for intensive chemotherapy, but low response rates and therapy-resistant relapse remain significant challenges. To optimise HMA efficacy, we must understand how resistance and relapse arise from cells that survive treatment. Here we combine single-cell multi-omic analysis with parallel colony-forming assays to link HMA-induced molecular heterogeneity with functional consequences in AML cells. HMAs, azacytidine (azacytidine) and decitabine (decitabine), induced global epigenetic heterogeneity associated with upregulation of inflammatory responses and cell death pathways in a subset of hypomethylated cells. Some AML cells maintained high DNA methylation during treatment, and these methylation-retaining cells had increased self-renewal capacity following decitabine, but not azacytidine. Molecular profiling of individual colonies revealed upregulated cholesterol biosynthesis as an adaptation to HMA treatment, and inhibition by rosuvastatin enhanced decitabine  effects in vitro and in vivo. Thus, HMA-induced heterogeneity has important implications for AML cell growth and statins are a candidate co-treatment strategy to delay or prevent HMA-resistant relapse.

overall_design: Leukaemia cell lines (MOLM-13 and MV-4-11) were treated with hypomethylating agents (HMAs) over 72 hours (doses at 0, 24 and 48 hours) with either decitabine (DAC), or azacytidine (AZA) and compared to untreated cells. At 72 hours, viable (propidium iodide negative) single cells were isolated by Fluoresence activated cell sorting (FACS), and analysed by scTEM-seq to measure global DNA methylation levels.

last: R Bond

last: Steffens Reinhardt

middle: K

last: Lê Cao


title: Loss of the C-terminus of p63 leads to an increased expression of extracellular matrix genes in keratinocytes due to a preferential binding of p63 to promoters

status: Public on Jul 22 2025

city: Rome

first: Artem

last: Smirnov

address: Via Montpellier 1

department: Dept. of Exper. Medicine

country: Italy

institute: University of Rome "Tor Vergata"

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Loss of the C-terminus of p63 leads to an increased expression of extracellular matrix genes in keratinocytes [RNA-seq]

summary: The transcription factor p63 is a master gene of epithelial development. p63 regulates expression of genes related to proliferation, differentiation and adhesion by binding epithelial enhancers. Biochemically, p63 interacts with chromatin via its DNA binding domain, while N-terminus is essential for the fine tuning of its transcriptional activity. However, the role of the C-terminus of p63 remains elusive. Here, we investigate the role of the C-terminal SAM domain of p63 in vivo. We generated Krt14-specific knock-out of the SAM domain (exon 13) of p63 which resulted in expression of the p63b isoform. Most of p63b expressing mice die 2-3 months after birth and show alteration of skin, adipose tissue and muscle morphology. Mechanistically, ChIP-seq analysis showed an increased binding of p63b to gene promoters. Further integration of transcriptome and genome occupancy analyses revealed that p63b binds more readily promoter regions of extracellular matrix (ECM) genes leading to their enhanced expression. Aberrant expression of ECM genes by p63b disrupts normal adhesion of keratinocytes to basal lamina triggering systemic inflammation and premature death. Altogether, our data suggest that C-terminus ensures p63 selectivity in enhancer binding to maintain physiological levels of extracellular matrix and adhesion proteins.

overall_design: RNA seq of epidermises or proliferating mouse keratinocytes isolated from newborn Trp63-Ex13fl/fl (p63alpha) and KRT14-Cre;Trp63-Ex13fl/fl (p63beta) mice.

first: Anna

middle: M

last: Lena

first: Eleonora

last: Candi


title: Loss of the C-terminus of p63 leads to an increased binding of p63 to promoters and histone acetylation [ChIP-seq]

overall_design: P63 and H3K27ac ChIP seq of proliferating mouse keratinocytes isolated from newborn Trp63-Ex13fl/fl (p63alpha) and KRT14-Cre;Trp63-Ex13fl/fl (p63beta) mice.


title: Upregulated cholesterol biosynthesis facilitates the survival of methylation-retaining AML cells following decitabine treatment [scNMT-Seq]

city: Newcastle

first: Heather

last: Lee

state: NSW

address: University Drive, Callaghan

country: Australia

institute: The University of Newcastle

summary: DNA hypomethylating agents (HMAs) are used to treat acute myeloid leukaemia (AML) and myelodysplasia patients who are unsuitable for intensive chemotherapy, but low response rates and therapy-resistant relapse remain significant challenges. To optimise HMA efficacy, we must understand how resistance and relapse arise from cells that survive treatment. Here we combine single-cell multi-omic analysis with parallel colony-forming assays to link HMA-induced molecular heterogeneity with functional consequences in AML cells. HMAs, azacytidine (AZA) and decitabine (DAC), induced global epigenetic heterogeneity associated with upregulation of inflammatory responses and cell death pathways in a subset of hypomethylated cells. Some AML cells maintained high DNA methylation during treatment, and these methylation-retaining cells had increased self-renewal capacity following DAC, but not AZA. Molecular profiling of individual colonies revealed upregulated cholesterol biosynthesis as an adaptation to HMA treatment, and inhibition by rosuvastatin enhanced DAC effects in vitro and in vivo. Thus, HMA-induced heterogeneity has important implications for AML cell growth and statins are a candidate co-treatment strategy to delay or prevent HMA-resistant relapse.

overall_design: HL-60 cells were treated with hypomethylating agents (HMAs) over 72 hours (doses at 0, 24 and 48 hours) with either Decitabine (DAC), or Azacytidine (AZA) and compared to untreated cells. At 72 hours, viable (propidium iodide negative) single cells were isolated by Fluoresence activated cell sorting (FACS), and analysed by scNMT-seq. This experiment was performed in 3 separate batches.

first: Danielle

middle: R

last: Bond

first: Sean

last: Burnard

first: Kumar

last: Uddipto

first: Kooper

middle: V

last: Hunt

first: Brooke

last: Harvey

first: Charley

last: Lawlor-O’Neill

first: Ellise

last: Roper

first: Sam

last: Humphries

first: Luiza

middle: S

last: Reinhardt

last: Murray

first: Nikola

last: Bowden

first: Anoop

last: Enjeti

first: Nicole

last: Verrills

first: Carlos

last: Riveros

first: Kim-Anh

middle: J


title: Upregulated cholesterol biosynthesis facilitates the survival of methylation-retaining AML cells following decitabine treatment [single_colony_TEM-Seq]

type: Methylation profiling by high throughput sequencing

summary: DNA hypomethylating agents (HMAs) are used to treat acute myeloid leukaemia (AML) and myelodysplasia patients who are unsuitable for intensive chemotherapy, but low response rates and therapy-resistant relapse remain significant challenges. To optimise HMA efficacy, we must understand how resistance and relapse arise from cells that survive treatment. Here we combine single-cell multi-omic analysis with parallel colony-forming assays to link HMA-induced molecular heterogeneity with functional consequences in AML cells. HMAs, azacytidine cytidine (azacytidine ) and decitabine (decitabine ), induced global epigenetic heterogeneity associated with upregulation of inflammatory responses and cell death pathways in a subset of hypomethylated cells. Some AML cells maintained high DNA methylation during treatment, and these methylation-retaining cells had increased self-renewal capacity following decitabine , but not azacytidine . Molecular profiling of individual colonies revealed upregulated cholesterol biosynthesis as an adaptation to HMA treatment, and inhibition by rosuvastatin enhanced decitabine  effects in vitro and in vivo. Thus, HMA-induced heterogeneity has important implications for AML cell growth and statins are a candidate co-treatment strategy to delay or prevent HMA-resistant relapse.

overall_design: Leukaemia cell lines (HL-60, MOLM-13 and MV-4-11) were treated with hypomethylating agents (HMAs) over 72 hours (doses at 0, 24 and 48 hours) with either Decitabine (DAC), or azacytidine cytidine (AZA) and compared to untreated cells. After 72 hours treatment, cells were seeded into MethoCult and cultured for 14 days. Individual colonies were picked and assessed by parallel TEM-seq and RNA-seq.

last: Huntreated

last: Steffens Reinhardt

last: Lê Cao


title: Transcriptomic Characterization Reveals Disrupted Medium Spiny Neuron Trajectories in Huntington's Disease and Possible Therapeutic Avenues [scRNA-seq]

city: Novato

last: Galicia Aguirre

address: 8001 Redwood Blvd

country: USA

institute: Buck Institute

summary: Huntington's Disease (HD) is a neurodegenerative disorder caused by an expansion of CAG repeats in exon 1 of the HTT gene, ultimately resulting in the generation of a mutant HTT (mHTT) protein. Although mHTT is expressed in various tissues, it significantly affects medium spiny neurons (MSNs) in the striatum, resulting in their loss and the subsequent motor function impairment found in HD. While HD symptoms typically emerge in midlife, disrupted MSN neurodevelopment plays an important role. To explore the effects of HD on MSN development, we differentiated induced HD pluripotent stem cells (iPSC) and isogenic control into neuronal stem cells, and then generated a developing MSN population encompassing early, intermediate progenitors, and mature MSNs. Single cell RNA sequencing (scRNAseq) revealed that the developmental trajectory of MSNs in our model closely emulated  the trajectory of fetal striatal neurons. However, in the HD MSN cultures, this process was by downregulating several crucial genes for required for proper MSN maturation, including ASCL1 and members of the DLX family of transcription factors. Our analysis also uncovered a progressive dysregulation of multiple HD-related pathways as MSNs matured, including the NRF2-mediated oxidative stress response and ERK/MAPK signaling. Using the transcriptional profile of developing HD MSNs, we searched the L1000 dataset for small molecules that induce an opposite gene expression pattern. Our analysis pinpointed numerous small molecules with known benefits in HD models, as well as previously untested novel molecules. A top novel candidate, Cerulenin, demonstrated a partial restoration of DARPP-32 levels and electrical activity in HD MSNs, while also modulating genes involved in in multiple HD related pathways.

overall_design: iPSC HD72 and isogenic controls (C116) were used for generate NSCs and MSNs. scRNAseq was performed on these cells using the 3' 10x platform.

first: Lisa

last: Ellerby

first: Kizito-Tshitoko

last: Tshilenge

first: Swati

last: Naphade


title: Transcriptomic Characterization Reveals Disrupted Medium Spiny Neuron Trajectories in Huntington's Disease and Possible Therapeutic Avenues [bulk RNA-seq]

overall_design: iPSC derived HD72 MSNs and isogenic controls (C116) were used for bulk RNAseq.

last: Galicia


title: Transcriptomic Characterization Reveals Disrupted Medium Spiny Neuron Trajectories in Huntington's Disease and Possible Therapeutic Avenues


title: Transcriptomic Characterization Reveals Disrupted Medium Spiny Neuron Trajectories in Huntington's Disease and Possible Therapeutic Avenues [Bulk RNA-seq treated with Cerulenin]

overall_design: iPSC derived HD72 MSNs and isogenic controls (C116) were treated with 250nM Cerulenin and collected for bulk RNAseq.


title: Therapeutic targeting of the GSK3b-CUGBP1 pathway in Myotonic Dystrophy

city: Cincinnati

first: Rebekah

last: Karns

state: OH

address: 3333 Burnet Ave

department: Gastroenterology, Hepatology, & Nutrition

institute: Cincinnati Children's Hospital Medical Center

summary: Myotonic Dystrophy type 1 (DM1) is a neuromuscular disease associated with toxic RNA containing expanded CUG repeats. Treating mice with the GSK3 inhibitor tideglusib corrected expression of 17% of DM1-related genes. correction of the GSK3β-CUGBP1 pathway in mice expressing long CUG repeats (DMSXL model) is important not only at prenatal and postnatal stage, but also beneficial in adult mice.

overall_design: Comparative expression of WT and HSA mice treated with either vehicle or GSK3 inhibitor tideglusib.

first: Lubov

last: Timchenko


title: Comparative transcriptome analysis for remodeling the cellulase activities in A. aculeatus

city: Khlong Luang

first: Wuttichai

last: Mhuantong

state: Pathum Thani

address: National Center for Genetic Engineering and Biotechnology (BIOTEC)

country: Thailand

institute: BIOTEC

summary: The aim of this study was to find candidate genes in A. aculeatus to improve the the cellulase production and function

overall_design: Transcriptome data of A. aculeatus strains with different abilities in degrading plant biomasses, cultured in control and cellulase-inducing conditions

first: Duriya

last: Chantasingh

first: Varodom

last: Chareonsawan

first: Salisa

last: Charoensri

first: Pongpannee

last: Phumikhet


title: The effect of melatonin on clock-regualted genes in renal tubular epithelial cell

city: Taipei

first: Yen-Sung

last: Huang

address: Academia Sinica, No.128, Sec2,

department: Institute of Biomedical Sciences

country: Taiwan

institute: Academia Sinica

summary:
The expression of clock genes are co-regulated by BMAL1 and CLOCK in all tissue including kidney.
Whether these clock-regualted genes can be affected by melatonin still unclaer.
To further examine the possible mechanism and biological consequence, we depleted BMAL1 or CLOCK with small interfering RNA (siRNA) and treated cells with melatonin.
Then, we used microarray analyses to identify clock genes regulated by melatonin in renal tubular epithelial cell.

overall_design: Human renal tubular epithelial cells (HK2) cells were transfected with 10 nmol/L specific siRNA oligonucleotides against BMAL1/CLOCK or treated with 10 nM melatonin. Total RNA was extracted from BMAL1/CLOCK-depleted cell or melatonin-treated HK-2 cells.

first: Yen

first: Hsin

middle: Y

last: Hsiech

first: Cheng

last: Guo

first: Chia

middle: C

last: Wu


title: Elevated systemic phenylalanine disrupts glutamate-dependent STING signaling in neutrophils and impairs cancer immunotherapy

status: Public on Jul 21 2025

city: Indianapolis

first: Yuan

last: Liu

state: IN

address: 410 W. 10th Street

institute: Indiana University

summary: Immune checkpoint inhibitors (ICIs) have transformed cancer therapy, yet acquired immune resistance remains a major barrier to durable response. Here, we identify a previously unrecognized immunometabolic axis in which elevated systemic phenylalanine (Phe) - driven by dietary intake or ICI-induced hepatic dysfunction - promotes immune evasion. Mechanistically, ICI-induced IL-6 and IFN-γ trigger proteasomal degradation of phenylalanine hydroxylase (PAH) via a TOPK-HECTD1 pathway in hepatocytes, leading to increased circulating Phe. Excess Phe suppresses antitumor immunity by impairing STING activation in tumor-associated neutrophils (TANs), through antagonism of glutamate-GRIK1-CaMKIV signaling. We uncover a key STING phosphorylation site (S324/326) essential for ER-to-Golgi trafficking and type I interferon responses, which is disrupted by Phe. These effects are independent of cGAS-cGAMP and define a glutamate-sensing checkpoint in neutrophil immunity. Therapeutically, restoring PAH function using liver-targeted synthetic RNA mimetics of HULC - a noncoding RNA shown to allosterically enhance PAH enzymatic activity - or activating GRIK1 with SYM2081 reprograms the tumor microenvironment, enhances CD8⁺ T cell function, and overcomes ICI resistance. This work reveals hepatic metabolic reprogramming as a central mechanism of immune escape and highlights new therapeutic opportunities to boost immunotherapy efficacy.

overall_design: This study utilized single-cell RNA sequencing (scRNA-seq) to investigate how elevated systemic phenylalanine (Phe), induced by dietary aspartame (APM), affects tumor-infiltrating immune cell populations during anti–PD-1 immunotherapy. Tumor-infiltrating immune cells were isolated from B16F10 melanoma tumors in C57BL/6 mice assigned to two dietary conditions: Chow diet + anti–PD-1 antibody and Aspartame diet + anti–PD-1 antibody. Mice were treated with anti–PD-1 antibodies to simulate immune checkpoint blockade, and tumors were harvested for analysis. Single-cell suspensions were generated from tumor tissues, and CD45⁺ immune cells were enriched by FACS. This experimental design enabled high-resolution analysis of how dietary Phe elevation reshapes the tumor immune microenvironment, with a particular focus on tumor-associated neutrophils (TANs) and their immunosuppressive programs under anti–PD-1 therapy.

first: Yajuan

last: Li

first: Chengcao

last: Sun

first: Zhao

last: Zhang

first: Leng

last: Han


title: CRISPR-Cas9 base editing to render CaMKIIδ phosphoresistant improves survival and cardiac function in heart failure

city: Dallas

first: kenian

last: chen

state: TX

address: 5323 Harry Hines Boulevard

department: Population and Data Science

institute: UTsouthwestern

summary:
We ablated the autophosphorylation site of CaMKIIδ (T287) using CRISPR-Cas9 adenine base editing technology.
Ten-weeks old C57Bl6 wildtype and CaMKIIδ T287A mice were subjected to either sham or severe transverse aortic constriction (sTAC) surgery (WT-Sham, WT-sTAC, T287A-Sham, T287A-sTAC; 3 biological replicates per group).
Two weeks after the surgery, hearts were harvested for RNA isolation and subsequent bulk RNA sequencing and gene expression profiling analysis.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for WT-Sham, WT-sTAC, T287A-Sham, and T287A-sTAC.

first: Simon

last: Lebek

first: Xurde

last: Caravia

first: Francesco

last: Chemello

first: Wei

last: Tan

first: John

last: McAnally

first: Kenian

last: Chen

first: Lin

last: Xu

first: Ning

first: Rhonda

last: Bassel-Duby

first: Eric

middle: N

last: Olson


title: CBX7 Promotes Lung Adenocarcinoma Metastasis by Transcriptionally Repressing SOCS3

city: Tianjin

first: Bei

last: Lan

state: 天津Tianjin

address: No22.Qixiangtai Rd.,Heping Dist,Tianjin P.R. China

country: China

institute: Tianjin Medical University

summary: In lung adenocarcinoma (LUAD), metastasis is a leading cause of mortality and notably tends to occur at an early stage of the disease. CBX7, a component of canonical Polycomb Repressive Complex 1 (PRC1) which mediates transcriptional repression, exhibits complex and context-dependent functions across different types of cancer. However, the roles of CBX7 in LUAD metastasis remain largely uncharacterized. Here we report that overexpression of CBX7 promotes, whereas its knockdown suppresses, LUAD cell migration and invasion in vitro. In vivo studies further confirm the pro-metastatic role of CBX7 in LUAD. Mechanistically, CBX7 suppresses the expression of SOCS3, which has been reported to be involved in cancer cell migration and invasion. At the molecular level, CBX7 binds to SOCS3 transcription start site (TSS) downstream region to establish monoubiquitination of histone H2A at lysine 119 (H2AK119ub), leading to transcriptional repression of SOCS3. Furthermore, knockdown of SOCS3 rescues the reduced migration and invasion caused by CBX7 depletion in LUAD cells. Together, our findings identify CBX7 as a positive regulator of LUAD metastasis and suggest its potential as a therapeutic target for LUAD treatment.

overall_design: Examination of gene expression changes in control and CBX7 overexpression A549 cells

first: Sirui

last: Huang


title: Fat promotes growth and invasion in a 3D microfluidic tumor model  of triple-negative breast cancer

city: Princeton

first: Celeste

last: Nelson

address: 25 William St

institute: Princeton University

summary: Diet influences the levels of small molecules that circulate in plasma and interstitial fluid, altering the biochemical composition of the tumor microenvironment (TME). These circulating nutrients have been associated with how tumors grow and respond to treatment, but it remains difficult to parse their direct effects on cancer cells. Here, we combine a three-dimensional (3D) microfluidic tumor model with physiologically relevant culture media to investigate how concentrations of circulating nutrients influence tumor growth, cancer cell invasion, and overall tumor metabolism. Human triple-negative breast cancer cells cultured in 2D under media conditions mimicking five different dietary states show no observable differences in proliferation or morphology. Nonetheless, those exposed to high-fat conditions exhibit increased metabolic activity and upregulate genes associated with motility and extracellular matrix remodeling. In the 3D microfluidic model, high-fat conditions accelerate tumor growth and invasion and induce the formation of hollow cavities. Surprisingly, the presence of these cavities does not correlate with an increase in apoptosis or ferroptosis. Instead, RNA-sequencing analysis revealed that high-fat conditions induce the expression of MMP1, consistent with cavitation via cell invasion. Mimicking the flow of circulating nutrients within the TME can thus be used to identify novel connections between metabolic states and tumor phenotype.

overall_design: Bulk RNA-seq of MDA-MB-231 cells cultured in Human plasma-like medium (HPLM) with additives that mimic five different dietary conditions: baseline (A), high-ketone (B), high-insulin (C), high-fat (F) and high-glucose ( G). Additionally, we have also done bulk RNA-seq of MDA-MB-231 cells cultured in DMEM (D).

first: Maryam

last: Kohram

first: Carolina

last: Trenado-Yuste

first: Molly

last: Brennan-Smith

first: Evelyn

last: Navarro Salazar

first: Pengfei

first: Jasmine

middle: E

last: Hao

first: Xincheng

first: Bharvi

last: Chavre

first: William

last: Oh

first: Sherry

middle: X

first: Susan

last: Leggett

first: Rolf-Peter

last: Ryseck

first: Joshua

middle: D

last: Rabinowitz


title: Systematic analysis of differential rhythmic kidney gene expression

first: Yen-Sung

summary: Many reports support a link between circadian rhythm and renal diseases. However, these dysregulated clock-controlled genes in kidney have mainly focused on the protein-coding genes. Here, we try to identify these circadian long-coding RNA (lncRNAs) in renal tissue.

overall_design: To obtain the rhythmic gene expression in mouse kidney, we performed RNA sequencing (RNA-seq) with RNA from mouse kidneys collected every 4 h respectively under light/dark (LD) cycle.

first: Yen

first: Hsin

last: Hsieh

first: Cheng

last: Guo

first: Chia

last: Wu


title: Phase I/II trial of encorafenib, cetuximab, and nivolumab in microsatellite stable, BRAFV600E metastatic colorectal cancer

city: New York

first: Anirban

last: Maitra

state: NY

address: Smilow 910, 522 1st Ave

department: Perlmutter Cancer Center

institute: New York University Grossman School of Medicine


title: The role of N6-Methyladenosine (m6A) methylation in pathological myopia

city: Guangzhou

first: Huiying

last: Song

address: Tianhejinsuilu

institute: Zhongshan Ophthalmic Center of Sun Yat-sen University

summary: To explore the role of N6-Methyladenosine (m6A) methylation in pathological myopia,we performed a comparative gene expression profiling analysis of RNA-seq data for vitreous fluid of pathological myopia patients.

overall_design: To explore the role of N6-Methyladenosine (m6A) methylation in pathological myopia,we separately collected 5 vitreous fluid of pathological myopia patients and the controls,established the RNA-seq library and then performed the library sequencing.We then performed gene expression profiling analysis using data obtained from RNA-seq.

first: Xiujuan

last: Zhao

first: Zhixi

last: Li

first: Lin

last: Lu


title: Hi-C identifies structural variation associated with resistance in paired patient-derived ovarian cancer models

city: Heidelberg

first: Bryce

last: Lim

address: In Neuenheimer Feld 280

country: Germany

institute: DKFZ

summary:
Purpose: To establish a bioinformatics pipeline for identifying structural variation in cancer cell lines using Hi-C.
Results: We were able to identify translocations as the primary genomic aberration in the PEO1 and PEO4 cell lines, while copy number alterations were the primary mutational process in the PEO14 and PEO23 cell lines.
Conclusions: The strategy we present can be widely applied to the analysis of structural variation in cancer, and the data we have generated provides valuable insight into the processes that occur upon treatment of ovarian cancer with cisplatin.

overall_design: Hi-C libraries of four previously-established paired high-grade serous ovarian cancer cell lines were generated and sequenced

first: Andrew

last: Holding

first: James

last: Brenton

first: Florian

last: Markowetz


title: Phase I/II trial of encorafenib, cetuximab, and nivolumab in microsatellite stable, BRAFV600E metastatic colorectal cancer [dataset 2]

summary: The BRAF inhibitor encorafenib and anti-EGFR antibody cetuximab modestly improve survival for patients with microsatellite stable (MSS) BRAFV600E metastatic colorectal cancer (mCRC), characterized by higher immune activation than MSS BRAFwild-type CRC. In this phase I/II study (NCT04017650) of 26 participants with MSS BRAFV600E mCRC who received encorafenib, cetuximab, and anti-PD-1 antibody nivolumab, we report an overall response rate of 50% (95% confidence interval (CI) 29-71) and median progression-free survival of 7.4 months (95% CI, 5.6-9.6).  Transcriptomic profiling of pretreatment biopsies and extracellular vesicle RNA (evRNA) isolated from plasma show enrichment of non-canonical MAP kinase signaling and immune activation signatures for responders. Complement pathway activation enriches in non-responder biopsies. On serial evRNA profiling, decreased MAPK signature and increased interferon gamma response signature associate with sustained treatment benefit.  MSS BRAFV600E mCRC with baseline MAP kinase activation and immune activation signatures may benefit from the triple combination but not with complement pathway activation.

overall_design: RNA sequencing was performed on baseline tissue samples from twelve cases using the KAPAr Stranded RNA-Seq kit with RiboErase (HMR) (KAPA, Roche, cat. # 08098140702) and libraries were sequenced on a NextSeq 500 sequencer (Illumina, San Diego, CA, USA). Raw reads quality and adapter sequences were checked using FastQC (v. 0.11.8, RRID:SCR_014583). Sequencing reads were mapped using STAR (RRID:SCR_004463)43 against the human genome build (UCSC hg38), and gene level quantification was performed with featureCounts (RRID:SCR_012919)

first: Van

last: Morris

first: Nourhan

last: Abdelfattah

first: Kimal

last: Rajapakshe

first: Kyuson

last: Yun

first: Scott

last: Kopetz


title: Phase I/II trial of encorafenib, cetuximab, and nivolumab in microsatellite stable, BRAFV600E metastatic colorectal cancer [dataset 1]

overall_design: Paired pre-treatment and post-treatment blood samples collected together from twenty-five patients were utilized for evRNA isolation and RNA sequencing as recently described. Briefly, evRNA was isolated from four milliliters of plasma by ultracentrifugation. RNA extraction was performed using the total exosome RNA & Protein Isolation kit (Invitrogen, cat # 4478545) and the SMART-Seq® v4 Ultra® low input RNA kit (Takara, cat. # 634891) was used for cDNA amplification.   Globin RNA and ribosomal RNA were depleted by the riboPOOLs gRNA/rRNA depletion kit (siTOOLsBiotech, cat. # dp-K096-001002). Library preparation was performed with the Nextera XT DNA Library Preparation Kit (Illumina, cat. # FC-131-1096) and libraries were sequenced in a NovaSeq6000 at the Advanced Technology Genomics Core at MD Anderson.


title: The Dream and MEC Complexes reinforce SPR-5; MET-2 maternal reprogramming to maintain the Germline-Soma distinction  [mep-1 RNAseq]

city: kennesaw

first: Brandon

middle: Scott

last: Carpenter

state: GA

address: 370 Paulding Avenue, Room 119

department: Molecular and Cellular Biology

institute: Kennesaw State University

summary: Proper regulation of tissue-specific gene expression is essential for cell fate determination and development. In Caenorhabditis elegans, the distinction between germline and somatic cell fates is partially established through maternally inherited histone modifications. During gametogenesis, germline genes acquire transcription-coupled chromatin marks such as histone methylation, which are inherited by the zygote and must be reprogrammed at fertilization to prevent inappropriate germline gene expression in somatic tissues. This maternal reprogramming is mediated by histone-modifying enzymes, including the demethylase SPR-5/LSD1 and the H3K9 methyltransferase MET-2/SETDB1. Together, these enzymes limit DNA accessibility to transcriptional machinery, thereby resetting the chromatin landscape in te newly formed zygote. Failure to reprogram inherited histone methylation, as in spr-5; met-2 mutants, results in the ectopic expression of MES-4-targeted germline genes in somatic tissues, leading to developmental delay and sterility. Here, we investigated whether transcriptional repressor complexes—the DREAM and MEC NuRD complexes—cooperate with SPR-5 and MET-2 to specify germline versus soma. Loss of DREAM or MEC NuRD components alone causes somatic expression of germline genes. Strikingly, combined loss with spr-5; met-2 enhances developmental arrest at the L1 stage and exacerbates germline gene misexpression. By re analyzing previous published ChIP-seq data, we confirmed direct binding of MEP-1 and LIN-35 to these misregulated genes. Our findings demonstrate that maternal reprogramming and conserved chromatin repressor complexes act synergistically to repress germline transcription in somatic tissues, ensuring proper somatic development and preventing soma-to-germline transformation.

overall_design: RNA-seq analysis on spr-5; met-2 L1 progeny from hermaphorites fed either control (L4440) or mep1 RNAi  to determine differentially expressed genes compared to L1 progeny from wild-type ( N2 strain) hermaphrodites fed control RNAi.

first: Sindy

last: Chavez

first: Jazmin

last: Dozier

first: Saahj

last: Gosrani

first: Sandra

last: Nguyen

first: Jovan

last: Brockett

first: Sarah

last: Blancher

first: Sydney

last: Morgan-Benitez

first: Juan

last: Rodriguez

first: Onur

last: Birol

first: Monica

last: Reeves

first: Karen

last: Schmeichel

first: David

last: Katz


title: Immune profiling of Chil4 KD mice during allergic airway inflammation

city: Manchester

first: James

middle: Edward

last: Parkinson

state: Greater Manchester

address: Oxford Road

department: DIIIRM

country: United Kingdom

institute: University of Manchester

summary: Nanostring Innate Immune Profiling of WT and Chil4 KD mice after chronic treatment with PBS or DRA allergens.

overall_design: In this study littermate WT and KD CHil4 KD mice were treated intranasally twice weekly with PBS or DRA allergens. Whole lung RNA was harvested and profiled using the Nanostring innate immunity panel.

first: Tara

last: Sutherland


title: ChIP-seq analysis of STAT1-WT and STAT1-K193R gastric cancer cells

city: Jinan

first: Duanrui

last: Liu

address: Address:No. 324, Jingwu Weiqi Road

institute: Shandong Provincial Hospital

summary: This dataset presents ChIP-seq profiles of STAT1 wild-type (STAT1-WT) and lactylation-deficient mutant (STAT1-K193R) in MGC803 gastric cancer cells. The study aims to investigate the impact of STAT1-K193 lactylation on chromatin binding patterns. Comparative analysis of STAT1 occupancy between the two cell lines provides insights into the regulatory roles of STAT1 post-translational modification in gastric cancer progression.

overall_design: Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) was performed in MGC803 cells stably expressing either STAT1-WT or STAT1-K193R. Cells were cross-linked, sonicated, and subjected to immunoprecipitation using anti-STAT1 antibody. Input DNA and IP samples were sequenced using the Illumina platform. Each condition was processed in biological replicates to ensure reproducibility.

first: Yanfei

last: Jia

first: Maoxiao

last: Feng

first: Yang

last: Ni

first: Yunshan

last: Wang

first: Guangyong

last: Zhang


title: Locus Coeruleus noradrenergic axon loss drives olfactory dysfunction in Alzheimer's disease

city: Munich

first: Felix

middle: L

last: Struebing

address: Feodor-Lynen-Str. 23

department: Center for Neuropathology

institute: University of Munich

summary: Alzheimer's disease (AD) often begins with non-cognitive symptoms such as olfactory deficits, which can predict later cognitive decline, though the mechanisms remain unclear. Pathologically, the brainstem locus coeruleus (LC), the main source of the neurotransmitter noradrenalin (NA) modulating olfactory information processing is affected ealy. Here we show early and distinct loss of noradrenergic input to the olfactory bulb (OB) coinciding with impaired olfaction in an AD mouse model, before appearance of amyloid plaques. Mechanistically, OB microglia recognize and phagocytose LC axons. Reducing phagocytosis genetically preserves LC axons and olfaction. Importantly, patients with prodromal AD display elevated TSPO-PET signals in the OB, similarly to AppNL-G-F mice. We further confirm early LC axon degeneration in post-mortem OBs in patients with early AD. Our findings reveal a mechanism linking early LC damage to hyposmia in AD, suggesting olfactory testing and neurocircuit imaging for early diagnosis and enable timely therapeutic intervention for Alzheimer's disease.

overall_design: rRNA-depleted, total RNA-seq of microglia isolated from mouse olfactory bulbs at 2 months of age (CD11b MACS beads), comparing APP-NL-G-F mice and WT

first: Felix L

first: Lars

last: Paeger

first: Carolin

last: Meyer

first: Jochen

last: Herms


title: SOX2 Drives Esophageal Squamous Carcinoma by Reprogramming Lipid Metabolism and Histone Acetylation Landscape

city: Shanghai

first: ruofei

last: dai

address: dong'an road 130

institute: Fudan University

summary: SOX2 is not only a pioneer transcription factor with critical roles in stem cell function and cell reprogramming but also a potent initiating oncodriver for a multitude of squamous cancers. How SOX2 exerts a potent oncogenic activity in squamous lineage is largely unknown. Here we uncovered a unique role of SOX2 in driving up global histone acetylation in various esophageal squamous cancer cells (ESCCs). Chromatin immunoprecipitation sequencing (ChIP-seq) analyses demonstrated that knockdown of SOX2 in ESCC cells resulted in a global down-regulation of histone acetylation and impaired about half of the super-enhancers. We engineered an ESCC SOX2-dTAG cell line that allowed rapid degradation of SOX2, and subsequent ChIP-seq confirmed a role of SOX2 in promoting global histone acetylation, beside its role in promoting local histone acetylation at SOX2 binding regions. Combined metabolic and transcriptional analyses revealed two mechanisms by which SOX2 drives up global histone acetylation in ESCCs: promoting the expression of a panel of histone acetyltransferases and reducing long chain fatty acid synthesis/elongation at least in part by repressing the expression of long-chain acyl-CoA synthase 5 (ACSL5), which in turn channels acetyl-CoA to histone acetylation. We demonstrated that ACSL5 knockdown downregulated fatty acid synthesis/elongation and enhanced histone acetylation, whereas overexpression of ACSL5 resulted in lipid accumulation, histone hypoacetylation, and tumor growth inhibition. Finally, we showed that SOX2 expression correlates negatively with ACSL5 and positively with histone acetylation in clinical esophageal squamous tumors. Altogether, our study uncovers a role of SOX2 in reprogramming lipid metabolism and driving histone hyperacetylation and super-enhancer function, providing new mechanistic insights of SOX2 acting as a potent oncodriver.

overall_design: ChIP-seq of the histone modification H4ac in KYSE-450 cell with dTAG induced SOX2 rapidly regradation in 3 or 24 hours. And use drosophila S2 cells as spike-in.

first: Zhen

first: Ruofei

last: Dai

first: Li

last: Kang

first: Huan

last: Yang

first: Zhaosu

last: Chen

first: Jianzhong

last: He

first: Lei

last: Shu

first: Yiting

last: Zhong

first: Yunfeng

first: Zhengyi

last: Hua

first: Yuanyong

last: Huang

first: Yunhan

last: Jiang

first: Jiwen

last: Li

first: Liyan

last: Xu

first: Fei

last: Lan

first: Shu-Hai

last: Lin

first: Jiemin

last: Wong


title: Effects of deleting Alg14, Hex1, Hex2, GPI1, or Hxk1 on changes of transcriptomic profiles in Beauveria bassiana

city: Fuzhou

first: Long-Bin

last: zhang

state: Fujian

address: Jianping Road

department: College of Biological Science and Engineering

institute: Fuzhou University

summary: Beauveria bassiana is a popular and eco-friendly biopesticide. N-acetylglucosamine (GlcNAc) is a building block of both insect exoskeleton and fungal cell wall. GlcNAc-metabolic related genes might play vital roles during B. bassiana pathogen-pest interaction. Previous studies in Candida albicans have demonstrated that a UDP-GlcNAc transferase unit (Alg14), beta-hexosaminidase (Hex1 or Hex2), N-acetylglucosaminyl transferase component (GPI1), and hexokinase (Hxk1) was involved in GlcNAc-related metabolism. Herein, we found each homology of Alg14, Hex1 or 2, GPI1, and Hxk1 in B. bassiana, and reported the alteration of transcriptomic profiles between wild-type strain and gene-deletion mutants grown on cuticle broth (CB) supplemented with 1% cuticle powder of Locusta migratoria exoskeleton, followed by shaking at 150 rpm for 5 days at 25 degree centigrade.

overall_design: irst, Ngs1-deletion mutants were constructed through homologous-recombination strategy; then, aliquots of 50 mL 10^6 conidia/mL cuticle broth (CB) containing 1% cuticle powder were incubated by shaking at 150 rpm for 5 days at 25 degree centigrade. The cultures were centrifuged by 13,200 g for 1 min at 4 degree centigrade. Hyphal cultures were collected and used for total RNA extracted; subsequently, the extracted RNA were sent to Novogene Company (Beijing, China) for RNA sequencing using Illumina NovaSeq X Plus.

last: Zhang

first: Zhi-Hao


title: Host transcriptomic responses of chicken embryos during Avian Pathogenic Escherichia coli infection reveal the significant role of the yolk sac in embryonic mortality

city: HONGKONG

first: JINGYAO

last: WANG

address: Hong Kong Kowloon Tat Chee Avenue

institute: CITYU

summary: Colibacillosis caused by avian pathogenic Escherichia coli (APEC) is a major disease syndrome in poultry with the yolk sac infection recognized as a leading factor contributing to embryonic mortality. Yolk sac is the initial site of infection, however its contribution in embryonic mortality at molecular level has remained unexplored. To address this critical gap, we conducted RNA sequencing (RNA-seq) to analyze the comprehensive in vivo transcriptomic profiles of yolk sac and embryonic liver from APEC-infected embryos, comparing dead embryos with those that survived and mock-infected controls, to uncover key differences in host responses in multiple scenarios. Our results revealed that dead embryos displayed significant pro-inflammatory cytokine activity and cellular senescence, disrupted lipid and energy metabolism, and compromised antioxidative defenses, particularly in the yolk sac. In contrast, surviving embryos exhibited a regulated inflammatory response, enhanced mitochondrial activity, robust antioxidative responses and tissue repair mechanisms, which likely underpinned its resilience. Notably, yolk sac showed positive correlation (r = 0.531) with the embryonic liver, but demonstrated more severe inflammation and metabolic dysregulation, thereby highlighting its heightened vulnerability. Furthermore, reactive oxygen species (ROS) levels, the balance of the inflammatory response, and yolk sac integrity are crucial determinants of embryonic survival, with mitochondrial dysfunction serving as a key regulator of host immune and metabolic adaptation. The insights provide a deeper understanding of the previously overlooked role of yolk sac compared to liver during APEC infection, offering potential avenues for improving host resilience and mitigating economic losses in poultry.

overall_design: RNA-Seq profiling of yolk sac and liver from APEC-infected embryos: A comparative analysis between infected dead, infected surviving, and mock-infected control groups

first: Surya

last: Paudel


title: ChAHP Displaces Transcriptional Regulators Through Active Chromatin Remodeling [RNAseq]

city: Basel

first: Fabio

last: Mohn

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

summary: Transcriptional control in eukaryotes relies on the coordinated action of chromatin-based regulatory mechanisms, including control of nucleosome occupancy and chromatin modifications. We previously identified the ChAHP complex – comprising the chromatin remodeler CHD4, transcription factor ADNP, and HP1 proteins – as a repressor of SINE B2 retrotransposons and site-specific regulator of CTCF engagement with chromatin. However, the molecular basis of these functions remained unresolved. Here, we show that ChAHP-associated CHD4 is essential for SINE B2 repression, while HP1 proteins are dispensable. We further demonstrate that CHD4’s remodeling activity is not required for chromatin binding, but is critical for both retrotransposon silencing and efficient CTCF antagonism. We propose ChAHP is a sequence-specific recruiter of chromatin remodeling activity, facilitating transcriptional control and localized modulation of chromatin architecture.

overall_design: RNAseq experiments for ADNP PXVxL and N-terminal mutants and for CHD4-ADNP wt and mutant fusions were performed independent triplicates in wt and Cas9-engineered mESC.

first: Josip

last: Ahel

first: Michaela

last: Schwaiger

first: Marc

last: Bühler


title: ChAHP Displaces Transcriptional Regulators Through Active Chromatin Remodeling

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

overall_design: Refer to individual Series


title: Double vulnerability of active-NRF2 Lung Squamous cell carcinoma to NRF2 and TRIM24

city: Madrid

first: Rafael

last: Torres

state: Madrid

address: Darwin 3

department: Bioinformatics for Genomics and Proteomics (BioinfoGP)

country: Spain

institute: CNB

summary: Lung squamous cell cancer (LUSC) is associated with very poor survival due to the lack of specific treatments. A common genetic alteration in LUSC involves mutations in NFE2L2 (also named NRF2) or its regulator, KEAP1, resulting in increased activity of the NRF2 transcription factor (TF). This study compares the requirement for active-NRF2 in LUSC cell lines. Although normal-NRF2 cells are more sensitive to oxidative stress, they do not require NRF2 for survival under non-stress conditions, while LUSC cells with active-NRF2 mutations depend on NRF2 for viability. NRF2 depletion in patient-derived organoid cultures with active-NRF2 as well as in xenografts with active-NRF2 triggers cell death. A CRISPRa/dCas9 screening for gene targets capable of rescuing cell survival in these cells identified TRIM24 as a gene whose expression rescues cell survival in NRF2-depleted active-NRF2 LUSC cells. Alongside oxidative stress, the lack of TRIM24 selectively contributed to the induction of cell death (apoptosis and ferroptosis) in active-NRF2 LUSC cells. Cells with a high NFE2L2/KEAP1 copy number ratio also undergo cell death. The increase in cell death observed upon TRIM24 depletion involves a reduction in AKT activity resulting from destabilization of the PI3Ka catalytic subunit. Notably, overexpression of PI3Ka rescues cell survival in TRIM24-depleted active-NRF2 cells. These findings point to novel therapeutic approaches in LUSC.

overall_design: The authors have investigated the relevance of the NRF2 (NFE2L2) pathway in lung squamous cell carcinoma (LUSC) with the aim to identify novel therapeutic strategies. They report frequent activation of the NRF2/KEAP1 axis in LUSC and suggest impact on resistance to stress conditions (in particular ROS-induced oxidative stress) and dependency of LUSC cells on active NRF2 signaling. Depletion of NRF2 using shRNA results in loss of cell viability in LUSC cells and patient-derived organoids which also translates in reduced in vivo growth in a cell line xenograft model. Using CRIPRa/dCas9 screening they subsequently identify potential mediators of NRF2 dependency and further investigate the role of TRIM24. In cells with activated NRF2 signaling the reduction of TRIM24 induces cell death through apoptosis and ferroptosis. The mechanism underlying cell death mediated by TRIM24 depletion involves reduction of AKT activity through post-translational regulation of PI3Ka levels. The authors suggest that these findings could have therapeutic implications in LUSC.

first: Miriam

last: Sanchez-Ortega

first: Antonio

last: Garrido

first: Lorena

last: Sanz

last: Torres-Perez

first: Carmen

last: Hernandez

first: Alvaro

last: Gutierrez-Uzquiza

first: Ming

last: Sound Tsao

first: Ana-Clara

last: Carrera


title: ChAHP Displaces Transcriptional Regulators Through Active Chromatin Remodeling [gNOMEseq]

overall_design: gNOMeseq experiments for ADNP PxVxL and N-terminal mutants were performed independent duplicates in mESC.


title: Transcriptional remodeling by OTX2 directs specification and patterning of mammalian definitive endoderm [CUTnTAG]

first: Ly-sha

last: Ee

address: 413 E 69th Street

institute: Weill Cornell Medicine

summary: We discovered a role for the transcription factor OTX2 in formation of mouse definitive endoderm (DE). We used CUT&TAG to map H3K27ac- and H3K4me1-bound genomic regions and identify OTX2-bound enhancers during directed differentiation of EpiSCs to Primitive Streak (PS) intermediates and DE

overall_design: Mouse EpiSCs were converted to PS and DE. OTX2 was depleted for 21hrs at induction of each stage by dTAG13 treatment and OTX2-dependent H3K27ac and H3K4me1 binding sites were mapped using CUT&TAG.

first: Matthias

last: Stadtfeld

first: Daniel

last: Medina-Cano

first: Alexander

last: Polyzos


title: Transcriptional remodeling by OTX2 directs specification and patterning of mammalian definitive endoderm [scRNA_PS_Meso]

summary: We discovered a role for the transcription factor OTX2 in formation of mouse definitive endoderm (DE). We determined the gene expression profiles during conversion of EpiSCs to Primitive Streak (PS) and Paraxial Mesoderm (PM) using scRNA-seq. We used dTAG13 to deplete OTX2 at  PS.

overall_design: Mouse EpiSCs were differentiated to Primitive Streak (PS) and Paraxial Mesoderm (PM) with or without dTAG13 added at primitive streak or 24hr DE stage to deplete OTX2 for further 48hrs.


title: Transcriptional remodeling by OTX2 directs specification and patterning of mammalian definitive endoderm [PS_CUTnRUN]

summary: We discovered a role for the transcription factor OTX2 in formation of mouse definitive endoderm (DE). We used CUT&RUN to map OTX2-bound genomic regions and identify OTX2-regulated genes during directed differentiation of EpiSCs to DE

overall_design: EpiSCs were converted to DE and live cells isolated by flow cytometry. OTX2 binding sites were mapped in mouse EpiSCs, Primitive Streak (PS), and definitive endoderm using CUT&RUN for HA in OTX2-HA tagged cell lines.


title: PARP inhibitors elicit distinct transcriptional programs in homologous recombination repair competent castrate resistant prostate cancer

city: Philadelphia

first: Steven

last: McMahon

state: PA

address: 233 S 10th St

department: Biochemistry and Molecular Biology

institute: Thomas Jefferson University

summary: Prostate cancer (PCa) is the second most lethal cancer in men in the United States. African American (AA) men have twice the incidence and death rate from the disease than European American (EA) men. Early-stage PCa is treated with hormone deprivation therapy, although patients frequently experience relapse. Advanced stage PCa is associated with increased expression and activity of the DNA damage/repair pathway enzyme, poly (ADP-ribose) polymerase 1 (PARP1). Furthermore, PARP1 inhibitors are FDA-approved for the treatment of advanced PCa tumors that carry mutations in components of a specific DNA damage/repair pathway termed homologous recombination repair (HRR). However, PARPi also provide benefit in model systems without HRR incompetencies. A number of different PARPi have now been developed, tested and approved for use in PCa. These inhibitors utilize multiple biochemical mechanisms of action and exhibit distinct potencies and toxicity profiles. While there is emerging evidence of differences in DNA damage/repair pathway enzyme expression between EA and AA men, PARP1 itself has not been fully explored in the context of race. This study hypothesized that 1) AA and EA PCa may respond differently to PARPi and 2) different PARPi may differentially impact the transcriptome, irrespective of HRR status. To test these hypotheses, PCa patient samples from a racially diverse cohort were examined to define race-based differences in PARP activity/expression. Additionally, biologically relevant doses of five clinically relevant PARPi were established across multiple PCa lines carrying different genetic backgrounds, HRR status, and hormone therapy sensitivities. Collectively, these findings demonstrate a link between racial background and PARP1 expression/activity and define a core transcriptional response that lies downstream of all five PARPi, while simultaneously defining transcriptional programs unique to each inhibitor. These findings broaden our understanding of the effector pathways downstream of individual PARPi and provide a compelling rationale for a broader exploration of the impact of race on the response to PARPi. They may also help refine personalized recommendations for use of specific PARPi.

overall_design: RNAseq profiling of prostate cancer cell line, C4-2, after receiving a vehicle control (DMSO) or one of the five clinical PARPi (Veliparib, Rucaparib, Olaparib, Niraparib or Talazoparib) at 72h post steriod depletion and 24h post PARPi treatment.

first: Moriah

last: Cunningham

first: Jasibel

last: Vasquez-Gonzalez

first: Samantha

last: Barnada

first: Salome

last: Tchotorlishvili

first: Latese

last: Jones

first: Hailey

last: Shankle

first: Tessa

last: Mulders

first: Namra

last: Ajmal

first: Charalambos

last: Solomides

first: Ayesha

middle: A

last: Shafi

first: Leonard

middle: G

last: Gomella

first: Wm

last: Kevin Kelly

first: Matthew

last: Schiewer


title: T-cell receptor/CD28-targeted Immunotherapeutics Generate Functional Melanoma- or HIV-specific Responses by Selectively Driving Naïve T-Cell Expansion

city: Mountain View

first: Kitt

last: Paraiso

state: CA

address: 320 Logue Ave.

department: Bioinformatics

institute: Cellecta, Inc.

summary: Adoptive cell transfer (ACT), an increasingly used immunotherapeutic approach for the treatment of cancer and infectious diseases, typically infuses antigen-specific CD8+ T cells obtained after ex vivo stimulation with patient-derived dendritic cells (DC) loaded with defined peptides. However, broader use of this approach is limited by logistical complexity, variability, cost, and inconsistency in cell quality. To overcome these limitations, we developed a dimeric protein scaffold-based antigen-presentation platform, Immuno-STAT (IST), which delivers peptide-specific TCR activation and costimulatory signaling to robustly expand highly functional antigen-specific CD8+ T cells. We demonstrate that delivering TCR and CD28 signals by IST selectively activates and expands highly functional cytotoxic CD8+ T cells from the naïve CD8+ T cell repertoire specific for the melanoma-associated MART-1 antigen and the HIV-associated SL9 antigen. While naïve MART-1-specific CD8+ T cells were expanded by both MART-1-peptide loaded DC and MART-1-specific IST, naïve SL9-specific CD8+ T cells were expanded only by SL9-specific IST and not by SL9-peptide loaded DC. By enabling ex-vivo expansion of naïve antigen-specific T cells without generation of autologous DC, IST may overcome the practical hurdles limiting the wider use of ACT and expand its use as a therapeutic strategy for both cancer and infectious disease.

overall_design: TCR Immunoprofiling of tetramer isolated or bulk samples. Samples are either left unstimulated, or stimulated for 25 days with peptide-loaded DC or 100nM immuno-STAT.

first: April

last: Mueller

first: Steven C

last: Almo

first: Harris

last: Goldstein


title: Stress alters hypothalamic gene expression in adolescent male hamsters

city: New Brunswick

first: Kevin

last: Moran

state: NJ

address: 84 Lipman Drive, Bartlett Hall Room 305B

institute: Rutgers University

summary: In hamsters, a two-week exposure to chronic social stress in adolescence causes acceleration of agonistic behavior, enhanced adult aggression, impaired waiting impulsivity, and higher food intake, body fat, and long-term increased body weight. In adult rodents, stress is accompanied by widespread alterations in gene expression in the brain. The present research examined transcriptomic changes in the lateral, dorsomedial, and arcuate nucleus of the hypothalamus caused by adolescent stress using RNA Tag-sequencing. In each region, there were approximately 250 differentially upregulated and 250 downregulated genes. Many of the most significantly affected genes have been associated with metabolism and sex hormone function. For example, in the lateral hypothalamus, melanocortin 3 receptor, growth hormone releasing factor, both involved in metabolic processes, and neuropeptide VF precursor, involved in growth hormone inhibitory hormone production, were among the most upregulated in stressed subjects. In the dorsomedial hypothalamus, neuropeptide W, involved in feeding cessation, was significantly downregulated in stressed animals. Across both regions, G-protein coupled receptor 50, involved in thermoregulation, sleep, and sex-related mood disorders, was significantly altered, but in opposite directions. In the arcuate nucleus, a number of blood brain barrier- and inflammation-related genes were altered as well. Furthermore, there were consistent patterns of genetic ensembles identified through gene ontology analysis and weighted gene correlation network analysis that were altered across each region. Many of these involved roles in RNA processing, DNA methylation, myelination and synaptic organization. These findings reinforce prior behavioral, hormonal, and metabolic changes observed in this developmental model, and help guide future directions of research related to the negative consequences of early life stress.

overall_design: RNAseq profiling of lateral, dorsomedial, and arcuate nucleus of the hypothalamus in hamsters chronically stressed or control  hamsters from PND 28 to PND 42. All subjects sacrificed on PND43

first: Tyler

last: Milewski

first: James

last: Curley

first: Yvon

last: Delville


title: Lipopolysaccharide alters cell communication at the maternal-fetal interface revealed by Single-cell RNA-sequencing

city: Chengdu

first: Ming

last: Zhang

state: Sichuan

address: Sichuan Agricultural University, Huimin Road, Wenjiang District

department: Animal Reproduction

institute: Sichuan Agricultural University, China

summary: Embryo implantation is a decisive process to pregnancy that highly relies on cell communication at the feto-maternal interface. Embryo implantation failure is commonly caused by gram-negative bacterial infection, therefore,  we investigated the effect of Lipopolysaccharides (LPS) on cell types, communication and its signaling pathways of the pregnant uterus (along with the embryo) during embryo implantation using a single cell RNA Sequencing. This study is the first to report the effect of LPS induced condition compared to the normal condition of pregnant uterus during embryo implantation.

sample_organism:
Mus musculus
Escherichia coli O111:B4

platform_organism:
Mus musculus
Escherichia coli O111:B4

overall_design: The mice were synchronized, allowed naturing mating, and LPS administered on 3rd day of pregnancy and uterine (along with embryos) samples were collected on 4.5 day of pregnancy and performed Single-cell RNA-Sequencing

first: Arab

last: Lund

first: Yutian

last: Zeng

first: Run

first: Hao

last: Li


title: ChAHP Displaces Transcriptional Regulators Through Active Chromatin Remodeling [ChIPseq]

first: Fabio

last: Mohn

overall_design: ChIPseq experiments for ADNP, CTCF and Pol III were performed in indepdendent biological duplicates or triplicates in wt and Cas9-engineered mESC.

first: Josip

last: Ahel

first: Michaela

last: Schwaiger

first: Marc

last: Bühler


title: RCC2 and CD24 Cooperate to Modulate Prostate Cancer Progression Through Vimentin Ubiquitination and β-Catenin Pathway Activation

city: Birmingham

first: Lizhong

last: Wang

address: 740 20th St S

institute: UAB

summary: CD24 plays a crucial role in tumor growth and metastasis, including in prostate cancer. While CD24 stimulates prostate cancer cell growth by controlling the ARF-NPM interaction and p53 inactivation, the mechanism of CD24-mediated metastasis remains elusive. This study identifies a direct interaction between CD24 and RCC2 with roles in prostate cancer cell proliferation and migration. Immunohistochemical analysis of primary prostate cancer samples showed expression of CD24 in 49% of samples and RCC2 in 82%, with a positive correlation between their protein levels. Their co-expression, particularly the binding of CD24 to the C-terminal domain of RCC2, supports their direct interaction, which may regulate cell motility and adhesion. Functional assays revealed that knockout (KO) of RCC2 in DU145 and PC3 prostate cancer cells inhibited cell proliferation but unexpectedly enhanced cell migration and invasion, while CD24 KO reduced proliferation and migration. Notably, dual KOs of CD24 and RCC2 led to a significant decrease in cell proliferation but showed mixed effects on migration, indicating a complex interplay between these proteins. In vivo, RCC2 KO in prostate cancer cells promoted spontaneous lung metastasis without significantly altering primary tumor growth, contrasting with CD24 KO, which reduced tumor growth and metastasis. Mechanistically, RCC2 was shown to ubiquitinate and degrade Vimentin, influencing cytoskeletal dynamics and migratory behavior. Furthermore, CD24 was found to ubiquitinate and degrade RCC2, leading to modulation of the β-catenin signaling pathway. RCC2 KO increased β-catenin activation and decreased the expression of its inhibitors AXIN2 and APC, while CD24 KO led to β-catenin inactivation. This opposing regulation of β-catenin signaling by CD24 and RCC2 underscores their differential roles in prostate cancer cell migration. These findings provide new insights into the molecular mechanisms underlying prostate cancer growth and metastasis and identify the CD24-RCC2 axis as a potential therapeutic target for controlling tumor growth and metastasis in prostate cancer.

overall_design: Total RNA expression by deep-sequencing in DU145 cells sorted for different levels of CD24 gene knockout and RCC2 gene knockot.

first: Runhua

last: Liu

first: Xuelian

last: Cui


title: Transcriptional profiling of cDC2 subsets in IFNAR∆CD11c mice treated with allergens

city: Wellington

first: Franca

last: Ronchese

state: Wellington

address: Gate 7 University of Wellington Central Services Building

department: FR

country: New Zealand

institute: Malaghan Institute of Medical Research

summary: Conventional type 2 Dendritic Cells (cDC2) in the skin are cell subsets primarily responsible for the priming of T-helper type 2 (TH2) responses in the draining LN. The local inflammatory milieu has been demonstrated to condition cDC2 to promote such responses. To characterise the cDC2 response to the cytokine IFN-I, we performed bulk RNAseq on sorted cDC2 subsets from IFNAR∆CD11c and IFNARWT mice following treatment with an allergen.

overall_design: IFNAR∆CD11c mice were treated with CTO-labelled inactivated N. brasiliensis larvae intradermally, and 48h later, cDC2 subsets carrying the labelled antigen were sorted from the skin draining LN using an Aurora CS for bulk RNAseq.

first: Greta

last: Webb

first: Kerry

last: Hilligan

first: Sam

middle: I

last: Old

first: Shiau-Choot

last: Tang

first: Olivier

last: Lamiable


title: Impact of intestinal ERβ on the colon transcriptome during colitis-induced tumor development

city: Solna

first: Cecilia

last: Williams

address: Tomtebodav 23

country: Sweden

institute: Karolinska Institute

summary: To understand how specifically intestinal ERβ impacts the transcriptome during colitis and tumor develpment, sequencing was perfromed on colon epithelium from AOM/DSS or vehicle treated mice, and tumors from treated mice.

overall_design: mRNA profiles of epithelial scrape and tumors from WT and ERβKOVIl mice on a C57BL/6J background, treated with AOM/DSS or vehicle, were generated by deep sequencing. 4-5 biological replicates were used.

first: Madeleine

last: Birgersson

first: Lina

last: Stepanauskaite

first: Linnea

last: Hases

first: Amena

last: Archer


title: RNA-seq analysis of kidney tissues in KMN and KM mice

city: shanghai

first: wenxin

last: feng

address: 1954 Huashan Road, Shanghai

institute: shanghai jiaotong university

summary: To explore the possible role of Nsd2 in kidney cancer, the gene expression profile of kisney tissues from KMN (Ksp-Cre; Myc OE/+; Nsd2 OE/+) and littermate KM (Ksp-Cre; Myc OE/+) mice was examined by RNA sequencing(RNA-Seq).

overall_design: Refer to individual Series.

first: Wenxin

last: Feng

first: Ningyuan

first: Li

last: Li


title: Engineering of novel DNA polymerase variants for single enzyme quantitative multiplex Reverse Transcription-PCR

city: Konstanz

first: Luisa

middle: Barbara

last: Huber

state: Baden-Württemberg

address: Universitätsstraße 10

department: Department of Chemistry

institute: Universität Konstanz

summary: Reverse transcription polymerase chain reaction (RT-PCR) has evolved as a widely used approach in biotechnology and molecular diagnostics. It represents a powerful tool for amplifying and analysing RNA molecules and has therefore found widespread applications in profiling gene expression, viral detection and the diagnosis of various diseases. Well‑established methodologies use viral reverse transcriptases (RTs) to transcribe RNA to cDNA and thermostable DNA polymerases (DNA pols) to amplify the resulting target sequence by PCR. This study reports on the development of novel Thermus aquaticus DNA polymerase I (Taq pol) variants that each are able to catalyse both steps simultaneously in a single tube without the need of viral RTs. In combination with their excellent thermostability (up to 95°C), the novel Taq pol variants are suitable for employment in dye- or probe-based RNA detection methods. Moreover, the herein reported Taq pol variants are the first DNA pols that are capable of performing multiplex detection of various RNA targets in a single tube with a single enzyme. Thus, discovery marks a significant advancement of current RT-PCR approaches and contributes simplifying and reducing costs in molecular diagnostics.

sample_organism: Severe acute respiratory syndrome coronavirus 2

overall_design: SARS-CoV-2 (in vitro RNA, purchased from European Commission Joint Research Centre (EURM-019)) was used for RT-PCR catalsyed by RT-Taq, Mut_RT, Taq pol V2, Taq pol V3 and Taq pol V2 IL. Respective cDNA was used to prepare DNA amplicon libraries which were analyzed by NGS

first: Luisa B.

first: Andreas

last: Marx

first: Virginie

last: Marchand


title: Genetic and biochemical analyses reveal direct interactions between LitR and genes important for Vibrio fischeri physiology, including biofilm production

city: Bloomington

first: Center for Genomics and Bioinformatics

last: IU

address: 1001 E Third St

department: Biology

institute: Center for Genomics and Bioinformatics

summary: Bacteria can link gene expression to population density to promote group behaviors using quorum sensing. Quorum sensing controls a multitude of bacterial processes such as virulence, motility, and biofilm formation. In Vibrio fischeri, the quorum sensing-dependent transcription factor LitR inhibits biofilm formation. A previous study showed that LitR modestly inhibits transcription of the bcs locus, which comprises the genes responsible for producing the cellulose polysaccharide. However, beyond that, the mechanism of LitR’s inhibitory effect on biofilm formation was unknown. Here, we find that LitR transcriptionally activates pdeV, which encodes a c-di-GMP phosphodiesterase that indirectly promotes cleavage of the large adhesive protein LapV from the surface of V. fischeri, leading to biofilm dispersal. LitR also induces transcription of the sensor kinase VF_A1016, which we determined to be important for biofilm inhibition. Like loss of LitR, loss of VF_A1016 modestly increased bcs transcription. Through chromatin immunoprecipitation sequencing (ChIP-seq), we found that LitR directly binds to the VF_A1016 and pdeV regulatory regions. In total, we identified 147 LitR binding sites in the genome and confirmed LitR’s transcriptional control over a subset of these putative regulatory targets. Of note, we determined that LitR induces transcription of the genes encoding the diguanylate cyclase VF_1200 and the glyoxylate shunt protein AceB and inhibits expression of the putative transcription factor TfoY. LitR also differentially regulates the response regulator ArcA in static and shaking conditions. These data define the mechanism of LitR regulation of genes involved in biofilm formation and the physiology of V. fischeri.

overall_design: Wild-type V. fischeri strain ES114, the ∆litR mutant, and the ∆qrr1 mutant were assessed after growth in LBS + 10 mM CaCl2 at 24°C to an OD600 of 1.0. The samples were then assessed by ChIP-seq using anti-LuxR (Vibrio campbellii) to pull down V. fischeri LitR. DNA bound to LitR were sequenced.

first: Brittany

last: Fung

first: Chase

last: Mullins

first: Douglas

middle: B

last: Rusch

first: Julia

last: van Kessel

first: Karen

last: Visick


title: CUT&Tag analysis of H3K36me2 in KN (Ksp-Cre; Nsd2 OE/+) and WT mice

summary: To identify the genes directly regulated by H3K36me2 on a genome-wide scale, we performed CUT&Tag assays using a H3K36me2 specific antibody in KN (Ksp-Cre; Nsd2 OE/+) and WT mice.

first: Feng

last: Wenxin

first: Liu

last: Ningyuan


title: Transcriptional remodeling by OTX2 directs specification and patterning of mammalian definitive endoderm.

city: New York

first: Ly-sha

last: Ee

summary: We discovered a role for the transcription factor OTX2 in formation of mouse definitive endoderm (DE). We used RNAseq to measure changes in gene expression and identify OTX2-regulated genes during directed differentiation of EpiSCs to Primitive Streak (PS) intermediates and DE

overall_design: Mouse EpiSCs were converted to PS; DE1 (24hrs from PS) and DE2 (48hrs from PS) . OTX2 was depleted for 21hrs at induction of each stage by dTAG13 treatment and OTX2-dependent genes were identified by bulk RNAseq.

first: Matthias

last: Stadtfeld

first: Daniel

last: Medina-Cano


title: Forward genetic screening in engineered colorectal cancer organoids identifies novel regulators of metastasis [crispr gRNA knockout screening 3]

first: Joshua

middle: Hunter

last: Rhoades

address: 3800 Spruce St

department: Vet School

institute: University of Pennsylvania

summary: Cancer is the second leading cause of death globally, and this is due primarily to metastatic dissemination to distal sites. Metastatic outgrowth requires that cancer cells delaminate from the primary tumor, intravasate, survive in circulation, extravasate, then migrate to and proliferate at a distal site. Recurrent genetic drivers of metastasis have remained elusive, suggesting that, unlike the initial steps of oncogenic transformation and primary tumor development, drivers of metastasis may be variable. Here, we develop a framework for interrogating pathways governing metastasis by applying CRISPR/Cas9-based forward genetic screening in a genetically defined tumor-organoid model of colorectal adenocarcinoma. We conduct in vitro screens for invasion and migration alongside orthotopic, in vivo screens for gain of metastatic potential in a syngeneic mouse model, identifying suppressors of metastasis both unique to the in vivo setting as well as common to both models. Specifically, we identify Ctnna1 and Bcl2l13 as bona fide metastasis suppressors acting through distinct mechanisms, with CTNNA1 loss promoting carcinoma cell invasion and migration through an atypical EMT-like mechanism, and BCL2L13 loss promoting cell survival after extracellular matrix detachment and non-cell-autonomous changes to macrophage polarization. Ultimately, this study provides a proof-of-principle that high-content forward genetic screening can be performed in tumor-organoid models in vivo and identifies novel regulators of colon cancer metastasis.

overall_design:
Engineered colorectal adenocarcinoma organoids were transduced with various sgRNA libraries and implanted into atleast 5 mice and resulting primary and metastatic lesions were harvested after 5-6 weeks. Primary and metastatic lesions were compared to one another and reference organoids collected pre-implantation
Please note that these data (along with GSE263580 and GSE263581) are in accompaniment of the previous single cell dataset GSE237980.

first: Christopher

last: Lengner

first: Zvi

last: Cramer

middle: H


title: PBK/TOPK mediates Ikaros, Aiolos and CTCF displacement from mitotic chromosomes and alters chromatin accessibility at selected C2H2-zinc finger protein binding sites

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

institute: MRC London Institute of Medical Sciences

summary: PBK/TOPK is a mitotic kinase implicated in haematological and non-haematological cancers. Here we show that the key haemopoietic regulators Ikaros and Aiolos require PBK-mediated phosphorylation to dissociate from chromosomes in mitosis. Eviction of Ikaros is rapidly reversed by addition of the PBK-inhibitor OTS514, revealing dynamic regulation by kinase and phosphatase activities. To identify more PBK targets, we analysed loss of mitotic phosphorylation events in Pbk–/– preB cells and performed proteomic comparisons on isolated mitotic chromosomes. Among a large pool of C2H2-zinc finger targets, PBK is essential for evicting the CCCTC-binding protein CTCF and zinc finger proteins encoded by Ikzf1, Ikzf3, Znf131 and Zbtb11. PBK-deficient cells were able to divide but showed altered chromatin accessibility and nucleosome positioning consistent with CTCF retention. Our studies reveal that PBK controls the dissociation of selected factors from condensing mitotic chromosomes and contributes to their compaction.

overall_design: ATAC-seq for flow-purified mitotic chromosomes derived from wild-type and Pbk KO mouse preB cells, four biological replicates each.

first: Andrew

last: Dimond

first: Do

last: Gim

first: Elizabeth

last: Ing-Simmons

first: Chad

last: Whilding

first: Holger

last: Kramer

first: Dounia

last: Djeghloul

first: Alex

last: Montoya

first: Bhavik

last: Patel

first: Sherry

last: Cheriyamkunnel

last: Brown

first: Pavel

last: Shliaha

first: Juan

middle: M

last: Vaquerizas

last: Merkenschlager

first: Amanda

last: Fisher


title: Forward genetic screening in engineered colorectal cancer organoids identifies novel regulators of metastasis [crispr gRNA knockout screening 2]

last: Rhoades

overall_design:
Engineered colorectal adenocarcinoma organoids were transduced with various sgRNA libraries and implanted into atleast 5 mice and resulting primary and metastatic lesions were harvested after 5-6 weeks. Primary and metastatic lesions were compared to one another and reference organoids collected pre-implantation
Please note that These data (along with GSE263580 and GSE263582) are in accompaniment of the previous single cell dataset GSE237980.

middle: J

last: Lengner


title: ZFTA fusion oncoproteins drive tumorigenesis through transcriptional condensates

city: Memphis

first: Stephen

middle: C

last: Mack

state: Tennessee

address: 262 Danny Thomas Place

institute: St. Jude Children’s Research Hospital

summary: Over 95% of ependymomas (EPNs) that arise in the cortex are driven by a gene fusion involving the zinc finger translocation associated (ZFTA) protein. Using super-resolution and lattice light sheet microscopy, we demonstrate that the most frequent fusion variant, ZFTA-RELA (ZR), forms dynamic nuclear condensates that are required for oncogene expression and tumorigenesis. Mutagenesis of ZR reveals a key intrinsically disordered region (IDR) that governs condensate formation. Condensate-modulating ZR IDR mutations impaired genomic occupancy at oncogenic loci, and inhibited the recruitment of transcriptional effector proteins, such as MED1, BRD4 and RNA polymerase II. Using nuclear magnetic resonance spectroscopy, we examined the protein structure of the critical zinc finger found in ZR, and characterized its significance for condensate formation, genomic binding, and oncogene activation. Our data leverages microscopy, genomics, cell biology, animal modeling, structural biology, and machine learning approaches to provide mechanistic insights into the processes that govern oncogene expression in ZFTA FO-driven tumors.

overall_design: RNAseq exepriments to decipher molecular mechanisms driving ZFTA-RELA target gene expression.

first: Srinidhi

last: Varadharajan

first: Amir

last: Arabzade


title: Forward genetic screening in engineered colorectal cancer organoids identifies novel regulators of metastasis [crispr gRNA knockout screening 1]

first: Joshua

overall_design:
Engineered colorectal adenocarcinoma organoids were transduced with various sgRNA libraries and implanted into atleast 5 mice and resulting primary and metastatic lesions were harvested after 5-6 weeks. Primary and metastatic lesions were compared to one another and reference organoids collected pre-implantation
Please note that these data (along with GSE263581 and GSE263582) are in accompaniment of the previous single cell dataset GSE237980.

first: Christopher

first: Zvi

last: Cramer


title: Genetic etiology and phenotypic characteristics of fetuses with 11q deletion (11q23.3-q25) syndrome

city: Shenzhen

first: Tong

last: Zhang

address: Longgang District Maternity & Child Healthcare Hospital of Shenzhen City

summary:
To investigate the clinical phenotype, genetic etiology, and diagnosis of 11q deletion (11q-) syndrome.
The differences and severity of fetal phenotypes may depend on the types and quantities of functional genes contained in fragments of different sizes.

overall_design: In this study, pregnant women were selected from prenatal testing in Longgang Maternal and Child Health Hospital of Shenzhen. After screening for prenatal serological analysis, noninvasive prenatal genetic testing screening (NIPS), chromosome karyotype analysis, and chromosome microarray analysis (CMA), 4 pregnant women diagnosed with 11q- syndrome were selected for retrospective analysis.

first: Weiqiang

last: Liu


title: SOX2 Drives Esophageal Squamous Carcinoma by Reprogramming Lipid Metabolism and Histone Acetylation Landscape (RNA-seq)

city: Shanghai

first: Yiting

last: Zhong

address: 130 Dong'an Road

institute: Fudan University

summary: SOX2 is not only a pioneer transcription factor with critical roles in stem cell function and cell reprogramming but also a potent initiating oncodriver for a multitude of squamous cancers. How SOX2 exerts a potent oncogenic activity in squamous lineage is largely unknown. Here we uncovered a unique role of SOX2 in driving global histone acetylation and demonstrated that SOX2 is required for the formation of about half of the super-enhancers in esophageal squamous cancer cells (ESCCs). Combined metabolic, chromatin and transcriptional analysis revealed at least two mechanisms by which SOX2 drives histone acetylation in ESCCs: promoting the expression of a panel of histone acetyltransferases and program fatty acid metabolism, which channels acetyl-CoA to histone acetylation by promoting the expression of multiple genes in fatty acid -oxidation and by repressing the expression of long-chain acyl-CoA synthase 5 (ACSL5) involved in fatty acid synthesis. We demonstrated that ACSL5 knockdown  downregulated fatty acid synthesis and enhanced histone acetylation, whereas overexpression of ACSL5 resulted in lipid accumulation, histone hypoacetylation, and tumor growth inhibition. Finally, we showed that SOX2 expression correlates negatively with ACSL5 and positively with histone acetylation in clinical esophageal squamous tumors. Altogether, our study uncovers a role of SOX2 in reprogramming lipid metabolism and driving histone hyperacetylation and super-enhancer function, providing new mechanistic insights of SOX2 acting as a potent oncodriver.

overall_design: RNA-Seq profiles of control and SOX2 knockdown KYSE450 cells were generated by deep sequencing, in triplicate, using Illumina Novaseq 6000

first: Zhen

last: Wang

first: Ruofei

last: Dai

first: Li

last: Kang

first: Huan

last: Yang

first: Yunpeng

first: Jiwen

last: Li

first: Liyan

last: Xu

first: Fei

last: Lan

first: Shu-Hai

last: Lin

first: Jiemin

last: Wong


title: SOX2 Drives Esophageal Squamous Carcinoma by Reprogramming Lipid Metabolism and Histone Acetylation Landscape (ChIP-seq)

overall_design: ChIP-seq for SOX2, H4ac, H3K27ac and H3K4me3  in control and SOX2 knockdown KYSE450 cells.


title: SOX2 Drives Esophageal Squamous Carcinoma by Reprogramming Lipid Metabolism and Histone Acetylation Landscape

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

overall_design: Refer to individual Series


title: Single-cell analysis defines heterogenous differentiation pathways of human innate T cells

city: Seoul

first: Suyeong

last: Park

address: 1, Gwanak-ro, Gwanak-gu, Seoul, Republic of Korea

department: College of Pharmacy

country: South Korea

institute: Seoul National University

summary: MAIT, NKT and γδ T cells are innnate-like T cells developed from thymic tissue. We used single cell RNA sequencing (scRNA-seq) to profile transcriptomic landscape of innate-like T cells in human thymus.

overall_design: Innate T cells from human thymic tissue were isolated by combination of Magentic-activated cell sorting (MACS) and Fluorescence-activated cell sorting (FACS) according to the presence or absence of tetramer binding affinity and analyzed using scRNAseq.


title: Forward genetic screening in engineered colorectal cancer organoids identifies novel regulators of metastasis

first: Joshua

last: Rhoades

overall_design: Engineered colorectal adenocarcinoma organoids expressing a control or Bcl2l13-targeted sgRNA were implanted into the ceca syngeneic mice. 2 replicate primary tumors from both genotypes were isolated and subjected to scRNA-seq. 2 liver metatases were isolated from sgBcl2l13-implanted mice. Control sgRNA cells were used as reference

last: Lengner


title: Forebrain assembloids support the development of fast-spiking human PVALB+ cortical interneurons and uncover schizophrenia-associated defects.

first: Ryan

last: Walsh

address: 430 E 67th St

department: Developmental Biology

institute: MSKCC

summary: Disruption of parvalbumin positive (PVALB+) cortical interneurons is implicated in the pathogenesis of schizophrenia. However, how these defects emerge during development is not well understood. The protracted maturation of these cells during postnatal development has made their derivation from human pluripotent stem cells (hPSCs) extremely difficult, precluding  hPSC-based disease modeling of their role in neuropsychiatric diseases. Here we present a cortical assembloid system that supports the development of PVALB+ cortical interneurons which match the molecular profiles of primary PVALB+ interneurons and display their distinctive electrophysiological features. Further, we characterized cortical interneuron development in a series of CRISPR-generated isogenic structural variants associated with schizophrenia and identified variant-specific phenotypes in cortical interneuron migration and the molecular profile of PVALB+ cortical interneurons. These findings reveal plausible mechanisms on how disruption of cortical interneuron development may impact schizophrenia risk and provide an exciting human experimental platform to facilitate the study of PVALB+ cortical interneurons.

overall_design: Cortical assembloids were generated by seperately patterning dorsal and ventral forebrain organoids using dual SMAD and WNT inhibition followed by Sonic activation for the ventral forebrain. Organoids were fused at day 30 to make assembloids and collected for scRNA seq at days 60, 75 or 125 via a papain dissociation.

first: Gregg

last: Crabtree

first: Kriti

last: Kalpana

first: So Yoon

last: Koo

first: Joseph

last: Gogos

first: Ilya

last: Kruglikov

first: Lorenz

last: Studer

first: Luz

last: Jubierre

first: Gabriele

last: Ciceri


title: YTHDF1 phase separation triggers the fate transsition of spermatogonial stem cells by activating IκB-NFκB-CCND1 axis [RNA-Seq]

first: Ji

last: Wu

address: No.800, Dongchuan Road, Minhang District

institute: Shanghai Jiao Tong University

summary: The expression profile data was obtained by RNA-Seq data.

overall_design: the expression profile of spermatogonial stem cells (SSCs) and neural stem cell-like cells (iNSCs)

first: Qian

last: Fang


title: RNA-seq of A549 cells transfected with miR-19a or miR-negative control

city: Tokyo

first: Yu

last: Fujita

address: Nishi-shimbashi

country: Japan

institute: The Jikei University Scho of Med

summary: To identify direct miR-19a target genes, we first performed RNA-seq of A549 cells that were transiently transfected with either pre-miR-19a and the negative control miRNA.

overall_design: A549 cells were transfected with miR-19a or miR-NC, and harvested for 24 h.


title: YTHDF1 phase separation triggers the fate transsition of spermatogonial stem cells by activating IκB-NFκB-CCND1 axis


title: Hypomethylating agents induce epigenetic and transcriptional heterogeneity with implications for acute myeloid leukemia cell self-renewal

city: Newcastle

first: Heather

last: Lee

state: NSW

address: University Drive, Callaghan

institute: The University of Newcastle


title: YTHDF1 phase separation triggers the fate transsition of spermatogonial stem cells by activating IκB-NFκB-CCND1 axis [MeDIP-Seq]

summary: We use m6A-seq to report the most comprehensive survey to date of mRNA in spermatogonial stem cells (SSCs) and neural stem cell-like cells (iNSCs)

overall_design: Examing 2 conditions, each with 3 replicates


title: YTHDF1 phase separation triggers the fate transsition of spermatogonial stem cells by activating IκB-NFκB-CCND1 axis [ChIP-Seq]

summary: We use ChIP-seq to report the most comprehensive survey to date of chromatin organization in spermatogonial stem cells (SSCs) and neural stem cell-like cells (iNSCs)

overall_design: Examination of CCND1 binding sites in SSCs and iNSCs


title: Cardiac adaptation to endurance exercise training requires suppression of GDF15 via PGC-1α

status: Public on Jul 20 2025

city: Boston

first: Sumeet

middle: Anand

last: Khetarpal

state: MA

address: 450 Brookline Ave

institute: Dana Farber Cancer Institute

summary: Endurance exercise promotes adaptive growth and improved function of cardiomyocytes, which is supported by increased mitochondrial activity. In skeletal muscle, these benefits are coordinated by the transcriptional protein peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PGC-1α). The importance of PGC-1α to exercise-induced adaptations in the heart has been unclear. Here, we show that deleting PGC-1α specifically in cardiomyocytes prevents the expected benefits from exercise and instead confers heart failure after just six weeks of training. Supporting this, rare genetic variants in the human PPARGC1A gene, which encodes PGC-1α, are associated with risk of heart failure in the UK Biobank. We identify the stress-induced cytokine growth-differentiation factor 15 (GDF15) as a key factor increased in PGC-1α–deficient hearts that contributes to this dysfunction. Blocking cardiac Gdf15 expression improves cardiac performance and exercise capacity in these mice. Finally, in human heart tissue, lower cardiomyocyte PGC-1α expression is associated with higher GDF15 and with fewer cardiomyocytes. These findings implicate a crucial role for cardiomyocyte PGC-1α in enabling healthy heart adaptation to exercise in part through suppression of GDF15.

overall_design: Heart total RNA from 4 groups of mice was studied. Group 1: wild-type mice maintained as sedentary (WT_Sed); Group 2: cardiomyocyte PGC-1α knockout mice maintained as sedentary (KO_Sed); Group 3: wild-type mice after 6 weeks of endurance training by voluntary wheel running (WT_Ex); Group 4: cardiomyocyte PGC-1α knockout mice after 6 weeks of endurance training by voluntary wheel running (KO_Ex). 5 male mice (age 14-16 weeks) were studied per group.

first: Bruce

last: Spiegelman

first: Anthony

last: Rosenzweig


title: Expression analysis of USF1/USF2-depleted B cell response to ionizing radiation

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

summary: Cancer results from the accumulation of critical genetic mutations and the loss of genomic stability. Upon genotoxic insult, cells rapidly activate p53-dependent programs that pause the cell cycle and direct either DNA repair or apoptosis. The long-term transcriptional programs that direct either cell recovery or removal are less well understood. We used RNA interference to investigate the potential of upstream stimulatory factor (USF) 1 and 2 stress-response transcription factors to drive long-term DNA damage responses in the p53-deficient mouse B lymphocyte cell line, M12. Microarray analysis revealed that simultaneously depleting cells of both USF1 and USF2 altered the expression of 755 genes (>1.50-fold change, <0.05 FDR), relative to cells expressing a scrambled shRNA. Ionizing radiation induced widespread and distinct changes in gene expression in control and USF knockdown cells. Seven days after irradiation, 3225 and 2798 genes were differentially expressed in control and USF-depleted cells, respectively, roughly half of which were not shared between the two cell types. Microarray findings were confirmed for a panel of genes responsive to USF knockdown and/or irradiation by RT-qPCR. USF depletion led to the widespread differential expression of genes critical for immune development and function, while impairing the ability to mount a long-term transcriptional response to IR-induced DNA damage. These findings shed further light on transcriptional responses to ionizing radiation that manifest over several days, and provide the first evidence that USF1 and USF2 play overlapping roles in shaping this poorly understood aspect of the DNA damage response.

overall_design: Microarray gene expression analysis in USF1/USF2 double knockdown and scrambled shRNA control M12 mouse B cells before ionizing radiation (IR) and at 1 and 7 days post-IR.

first: Kimberley

middle: S

last: Bellingham-Johnstun

first: Jennifer

last: Stone

first: John

middle: R

last: King

first: Kevin

last: Gerrish

first: Pierre

last: Bushel

first: Michael

last: Sikes


title: Change of the mRNA level upon Puromycin treatment

first: Yoon Ki

last: Kim

address: Anam-ro 145, Seongbuk-gu

institute: Korea University

summary: Change in the levels of mRNAs upon Puromycin treatment were examined to analyze the mRNA population(s) affected directly or indirectly by global translation

overall_design: Two-independent replicate of comparison between two mRNA sets obtained Puro-treated vs. -untreated cells

first: Incheol

last: Ryu

first: Junho

last: Choe

first: Yoon

middle: K


title: ATAC-Seq of liver in cancer cachexia

city: Neuherberg

first: Peter

last: Weber

address: Ingolstädter Landstraße 1

institute: Helmholtz Zentrum München

summary: To study the response in the liver to cachectic and weight-stable cancer, we performed ATAC-sequencing of hepatocyte nuclei that were isolated using the INTACT methodology of weight stable NC26, pre-cachectic C26, cachectic C26, weight-stable MC38 and cachectic 8025 tumor bearing mice as well as their respective PBS controls.

overall_design: We implanted  cachexia-inducing tumor cells (C26, 8025) or tumor cells that give rise to weight-stable cancer (NC26, MC38) into syngenic Hep-INTACT mice. Livers were collected once a body weight loss of >10% was reached for C26 and 8025 tumor bearing animals at zeitgeber zeit (ZT) 9.

first: Mauricio

last: Berriel Diaz

first: Doris

last: Kaltenecker

first: Soren

last: Fisker Schmidt


title: CAR T Cell Sytotoxic Supernatant Stimulates Monocytes to Drive Cytokine Storm

city: Changchun

first: lei

last: qian

state: Jilin

address: Number 71,Xinmin Street,

department: cancer center

institute: First Hospital of Jilin Unniversity

summary: Chimeric antigen receptor (CAR) T cell-therapy is substantially constrained by cytokine release syndrome (CRS). The precise mechanisms underlying CAR T cell-therapy-associated CRS remain elusive. Here, we show that CAR T cell-induced tumor cytotoxicity activates monocytes to release IL-1β, IL-6, and TNF-α, key inflammatory cytokines driving CRS, via monocyte contact-independent manner.

overall_design: THP-1 cell line was stimulated with PBS, Lipopolysaccharides, Mock T+Raji or CART+Raji supernatant,then THP-1 cells were collected for RNAseq

first: Lei

last: Qian

first: Jianting

last: Xu

first: Xue

last: Yu

first: Xin

last: Zhou

first: Jiuwei

last: Cui


title: Transcriptional profiling of liver in cancer cachexia

summary: To study the response in the liver to cachectic and weight-stable cancer, we performed RNA-sequencing of whole liver nuclei and hepatocyte nuclei that were isolated using the INTACT methodology of weight stable NC26, pre-cachectic C26, cachectic C26, weight-stable MC38 and cachectic 8025 tumor bearing mice as well as their respective PBS controls.


title: RNA Seq of hearts upon hepatocyte-specific overexpression of REV-ERBα in cancer cachexia

summary: We evaluated the transcriptional response in the heart upon hepatocyte-specific overexpression of REV-ERBα in the C26 cancer cachexia model.

overall_design: We injected AAV intravenously that express either GFP or REV-ERBα  under the control of the hepatocyte specific promoter Tbg, followed by a subcutaneous transplantation of C26 tumor cells 10 days later. Non-tumor bearing mice received a PBS injection


title: Interferon-induced immunoproteasomes disturb neuronal metabolism and drive neurodegeneration in multiple sclerosis [RNS_Seq3_Nuclei]

city: Hamburg

first: Marcel

middle: Seungsu

last: Woo

state: Hamburg

address: Falkenried 94

department: Neurology

institute: UKE

summary: In this study, we investigated the proteasome composition and activity of neurons in CNS inflammation. Therefore, we investigated the multiple sclerosis mouse model and IFNy treated neurons. Thereby, we identified that the immunoproteasome leads to proteasomal dysfunction in neurons with subsequent accumulation of proteins that lead to ferroptosis.

overall_design: Here, we analyzed the mRNA expression of neurons during acute EAE 15 days after active immunization. We isolated the neuronal nuclei by flow cytometry sorting from the spinal cords of the mice. Thereby, we can seperate non-neuronal NeuN negative from neuronal NeuN positive nuclei.

first: Manuel

last: Friese


title: Interferon-induced immunoproteasomes disturb neuronal metabolism and drive neurodegeneration in multiple sclerosis [RNA_Seq1_Proteasome]

overall_design: Here, we analyzed neurons that overexpress a mScarlet control or the proteasomel subunits PSMB5 or PSMB8. Overexpression was achieved by lentiviral transduction at 7 d.i.v, the cells were harvested after an additional 10 d.i.v.


title: Interferon-induced immunoproteasomes disturb neuronal metabolism and drive neurodegeneration in multiple sclerosis [RNA_Seq2_IFNG]

overall_design: Here, we analyzed neurons that were continously exposed to IFNy in comparison to control neurons. Continous IFNy exposure was achieved by lentiviral overexpression of Ifng.


title: Comparative Transcriptomic Analyses within FiveDevelopmental Stagesof the Mushroom Oudemansiella raphanipes

city: Lanzhou City

first: Lan

middle: Lan

state: Anning District

address: Northwest Normal University, Shi Street, Anning District, Lanzhou City, Gansu Province, China

department: College of Life Sciences

institute: Northwest Normal University

summary: In this paper, we have employed transcriptomic analysis as a pivotal tool to dissect the molecular landscape across the quintet of growth and developmental phases exhibited by Oudemansiella raphanipes. Our investigation has not only unveiled a suite of critical differentially expressed genes but also shed light on the nuanced nutritional attributes intrinsic to this fungal species. These findings promise to furnish fresh insights, serving as a beacon for the enhanced comprehension of O. raphanipes biology.

overall_design: Comparative gene expression profiling analysis using data obtained from RNA-seq of fifteen samples in the five growth stages

first: Yanjun

last: Ma

first: Lanlan

first: JingMing

last: Zhang

first: YongXiang

last: Dang


title: An intrinsically disordered region of Drosha selectively promotes miRNA biogenesis, independent of tissue-specific Microprocessor condensates

city: Chevy Chase

first: Katherine

last: McJunkin

state: Maryland

address: 3714 Cardiff Court

institute: NIH/NIDDK Intramural Research Program

type: Non-coding RNA profiling by high throughput sequencing

summary: Precise control of miRNA biogenesis is of extreme importance, since mis-regulation of miRNAs underlies or exacerbates many disease states. The Microprocessor complex, composed of DROSHA and DGCR8, carries out the first of two cleavage steps in canonical miRNA biogenesis. Despite recent advances in understanding the molecular mechanism of Microprocessor, the role of N-terminal regions of DROSHA is less characterized due their high intrinsic disorder. Here we demonstrate that Microprocessor forms liquid-liquid phase separated (LLPS) condensates in select tissues in C. elegans.  We find that an intrinsically disordered region (IDR) near the N-terminus of DRSH-1/DROSHA is required for normal development and biogenesis of a subset of miRNAs.  Despite the known role of IDRs in LLPS, the role of the DRSH-1 IDR in miRNA biogenesis and development is genetically separable from its contribution to granule formation.  A cis region of an IDR-dependent miRNA confers IDR-dependence to another miRNA, suggesting that the IDR may recognize sequences or structures in the miRNA transcript. Future studies will further elucidate the specificity of this interaction and the putative role of Microprocessor condensates.

overall_design: small RNA sequencing performed using NEBNext kit followed with size selection in different deletion mutants of drsh-1 in C.elegans.

first: Bing

last: Yang

first: Brian

last: Galleta

first: Rima

last: Sakhawala

first: Nasser

last: Rusan


title: RNA-seq and ChIP-seq analysis of H3K27ac, H3K27me3, H3K9me2, and JMJD1A in 3T3-L1 cells and ChIP-seq analysis of NFIC in imSVF cells.

city: Akita

first: Yoshihiro

last: Matsumura

state: Akita

address: Hondo 1-1-1

department: Biochemistry and Metabolic Science

institute: Akita University Graduate School of Medicine

summary: Adipose tissue remodels via hypertrophy or hyperplasia in response to nutrient status, but the mechanisms governing these expansion modes remain unclear. Here, we identify a nutrient-sensitive epigenetic circuit linking glucose metabolism to chromatin remodeling during adipogenesis. Upon glucose stimulation, α-ketoglutarate (α-KG) accumulates in the nucleus and activates the histone demethylase JMJD1A to remove repressive H3K9me2 marks at glycolytic and adipogenic gene loci, including Pparg. JMJD1A is recruited to premarked promoter chromatin via NFIC, enabling carbohydrate-responsive element-binding protein (ChREBP) binding and transcriptional activation. This feedforward mechanism couples nutrient flux to chromatin accessibility and gene expression. In vivo, JMJD1A is essential for de novo adipogenesis and hyperplastic expansion in visceral fat under nutrient excess. JMJD1A deficiency impairs hyperplasia, exacerbates adipocyte hypertrophy, and induces local inflammation. These findings define a glucose–α-KG–JMJD1A–ChREBP axis regulating depot-specific adipogenesis and uncover a chromatin-based mechanism by which glucose metabolism governs adaptive adipose tissue remodeling.

overall_design: Total RNA isolation followed by next-generation sequencing. ChIP using anti-H3K27ac, anti-H3K27me3, anti-H3K9me2, anti-JMJD1A, or anti-NFIC antibody followed by next-generation sequencing.

first: Juro

last: Sakai


title: Microarray, RNA-seq, and ChIP-seq data of 3T3-L1 cells

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

overall_design: Refer to individual Series


title: Expression data of glucose-restricted or IDH3-knocked down 3T3-L1 cells.

overall_design: IDH3 target genes in 3T3-L1 cells were analyzed.