title: High-Throughput Drug Discovery for a Rare Neurological Disorder: Uncovering a Novel Therapeutic Opportunity for the 19q12 Autism Spectrum Disorder [post treatment entrectinib patient data]

status: Public on Mar 24 2025

city: Palo Alto

first: Drishti

last: Guin

address: 1804 Embarcadero Rd Ste #201

institute: Transcripta Bio

summary: Discovering new and viable therapies for genetic diseases is a time consuming and cost intensive process. This is even more challenging for rare disorders that affect a small fraction of the population and do not incentivise research and development in the traditional drug discovery lifecycle. There is therefore a need for scalable and efficient solutions for discovering novel therapies for these rare disorders. In this study, we highlight how a high-throughput drug discovery engine was utilized to uncover drugs at scale that normalized the signature for a rare neurological neurodevelopmental disease, 19q12 autism spectrum disorder associated with deficiencies in ZNF536 and TSHZ3. We do this by uncovering and understanding the full 360o view of the biological impact of the drug in a relevant cell line via transcriptomics. This platform, in combination with a statistically viable n-of-1 trial, was able to quickly uncover and utilize a novel therapeutic potential of a previously approved drug for a patient living with from 19q12 autism spectrum disorder.

overall_design: RNA-seq profiling of whole blood samples from patient (pre- and 3 and 6 months post-treatment with Entrectinib and a sibling.

first: Ursula

last: Haditsch

first: Joseph

last: Bellucci

first: Sabine

last: Topka

first: Katherine

last: Dyer

first: Gabriel

middle: A

last: Rivera Del Toro

first: Michael

last: Blanco

first: Natalie

middle: F

last: Downs

first: Nicole

last: Perfito

first: Christopher

last: Moxham


title: High-Throughput Drug Discovery for a Rare Neurological Disorder: Uncovering a Novel Therapeutic Opportunity for the 19q12 Autism Spectrum Disorder [DRUGseq]

state: CA

country: USA

type: Expression profiling by high throughput sequencing

overall_design: RNA-seq profiling of response of NGN2-derived glutamatergic neurons to Entrectinib at 10 concentrations using DRUG-seq.

middle: J

middle: E

middle: R

middle: M


title: High-Throughput Drug Discovery for a Rare Neurological Disorder: Uncovering a Novel Therapeutic Opportunity for the 19q12 Autism Spectrum Disorder [19q12 neurons baseline data]

overall_design: RNA-seq profiling of a 19q12 patient iPSC-derived neurons at 5 timepoints during neuronal differentiation, wildtype neurons treated with Entrectinib at 10 concentrations and whole blood of patient pre- and post-treatment with Entrectinib.


title: Pre-existing intratumoral stem-like CD8+ T-Cells drive radiotherapy-induced tumor control

city: Zürich

first: Hakan

last: Köksal

address: Winterthurerstrasse 190

department: Institute of Experimental Immunology

country: Switzerland

institute: University of Zurich

summary: To evaluate how intratumoral CD8+ T-cells are influenced by radiotherapy, we performed single-cell RNA sequencing of CD8+ T-cells sorted from MC38-OVA tumors 6 days after radiotherapy (single dose, 20Gy).

overall_design: Intratumoral CD8+ T-cells (live, CD45+, CD8+) were isolated by fluorescence-activated cell sorting (FACS) 6 days after radiotherapy. We used four conditions: irradiated (RT, 8 mice), untreated (UNTR, 8 mice), and two groups where lymphocyte infiltration was blocked with FTY720, labeled RT+FTY (8 mice) and UNTR+FTY (7 mice). Cells from each sample were labeled with the BD Single-Cell Multiplexing Kit and pooled based on their respective conditions. Conditions with FTY and without were sequenced at different times.

first: Maries

last: van den Broek


title: Effect of mtDNA on MDSCs

city: Bellinzona

first: Andrea

last: Alimonti

address: Via vela 6

department: Molecular Oncology

institute: Institute of oncology research

summary: Mitochondrial dysfunction is a hallmark of cellular senescence. Mitochondrial DNA (mtDNA) functions as a damage-associated molecular pattern that activates the innate immune system when released extracellularly. We examined whether senescent cells release mtDNA into the extracellular space and the consequences of this exogenous mtDNA in innate immunity. Both primary senescent cells and tumor cells undergoing therapy-induced senescence release mtDNA into the extracellular space. In vivo cross-species xenograft models using human prostate cancer cells in immunocompromised mice demonstrated the selective uptake of human mtDNA by mouse polymorphonuclear myeloid-derived suppressor cells (PMN-MDSCs) within the tumor microenvironment (TME). In vitro trans-well experiments confirmed the uptake of mtDNA by mouse PMN-MDSCs through extracellular vesicles (EVs). Internalized mtDNA enhanced the immunosuppressive activity of PMN-MDSCs via cGAS-STING-NF-_B activation, promoting tumor progression. Mechanistically, mtDNA released from senescent cells was mediated by voltage-dependent anion channels (VDAC), and pharmacological inhibition of VDAC reduced extracellular mtDNA levels, reversing PMN-MDSC-driven immunosuppression and improving the efficacy of chemotherapy in prostate cancer models. Thus, inhibiting mtDNA release may enable reprogramming of the immune suppressive microenvironment in patients treated with chemotherapy.

overall_design: After 4 days of differentiation of BM-derived MDSCs, we treated with mtDNA or not at the concentration of 250 ng/ml for 12h. After the treatment the RNA was isolated for sequencing.

first: Martina

last: Troiani


title: Staphylococcus epidermidis uses the SrrAB regulatory system to modulate oxidative stress and intracellular survival in mouse macrophage cell line Ana-1

city: Dali

first: chunjing

last: Zhao

state: Yunnan

address: wang hua street 22

department: Basic Medicine

country: China

institute: Dali University

summary: The two-component system (TCS) SrrAB responds to the oxidative stress in Staphylococcus epidermidis. To study its regulatory function in oxidative stress, a srrAB deletion mutant (∆srrAB) was constructed using S. epidermidis strain 1457 (SE1457) as the parent strain. Compared to SE1457, the viable cell counts of the ∆srrAB mutant significantly decreased in the post-stationary phase culture, coinciding with a sharp increase in ROS accumulation. The impaired growth of the ∆srrAB mutant was partially restored by shifting the culture from oxic to microaerobic conditions. Consistently, growth of the ∆srrAB mutant in TSB medium containing H2O2 was notably inhibited compared to parent strain SE1457, and the mutant showed significantly decreased resistance (100- to 1000-fold) to H2O2 and CHP in both oxic and microaerobic conditions, which was fully rescued by the addition of ROS inhibitor DIP. Furthermore, deletion of srrAB resulted in decreased intracellular survival in the Ana-1 macrophages due to intracellular ROS accumulation. Complementation of srrAB in the ∆srrAB mutant restored ROS resistance and intracellular survival to wild-type levels. RNA-seq analysis revealed that srrAB deletion affected the transcription levels of 610 genes, including those involved in oxidative stress, respiratory and energy metabolism, and transition ion homeostasis. These findings were corroborated by quantitative real-time reverse transcription-PCR (qRT-PCR). In the ∆srrAB mutant, expressions of ROS-scavenging genes katA, ahpC, scdA, serp1797 and serp0483 were downregulated compared to SE1457. Electrophoretic mobility shift assay further demonstrated that phosphorylated SrrA bound to the promoter regions of srrAB, katA, ahpC, scdA, serp1797 and serp0483 genes. This study elucidates that in S. epidermidis, SrrAB is the first TCS to sense and respond upon the oxidants, directly regulating transcription levels of the genes involved in ROS scavenging and ion homeostasis, thereby facilitating S. epidermidis detoxification of ROS and adaption to the commensal environment.

overall_design: To assess the oxidative stress response of srrAB in S. epidermidis, a srrAB deletion mutant of the SE1457 strain was constructed by allelic replacement using the temperature-sensitive plasmid pKOR1. RNA-Seq was performed to compare the transcriptional profile of ∆srrAB with that of SE1457. We then used the data obtained from RNA-seq for gene expression profiling to analyze the differences in oxidative stress-related genes between ∆srrAB mutant and SE1457 wild strains.

first: Chunjing

first: Lian

last: Qian

first: Youcong

last: Wu


title: NR2F2 regulation of interstitial cell fate in the embryonic mouse testis and its impact on differences of sex development [ChIP-Seq]

city: Durham

first: Humphrey

middle: Hung-Chang

last: Yao

state: NC

address: 111 TW Alexander Drive

institute: NIEHS/NIH

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Testicular fetal Leydig cells are specialized for androgen production during embryogenesis. Testosterone is essential for regulating sex differentiation, spermatogenesis, and fertility. Deficiencies in Leydig cell differentiation can lead to various disorders of sex development and male reproductive conditions, such as ambiguous genitalia, hypospadias, cryptorchidism, and infertility. Understanding the differentiation of fetal Leydig cells is essential for comprehending male sexual differentiation, reproductive health, and fertility.  Fetal Leydig cells originate from proliferating progenitor cells in the gonadal interstitium, marked by genes like Arx, Pdgfra, Tcf21, Wnt5a, and Nr2f2 (COUP-TFII). However, the precise mechanisms governing the transition from interstitial cells to Leydig cells remain elusive. Through integrated approaches involving animal models and multiomics, we have demonstrated that fetal Leydig cells originate from a COUP-TFII positive non-steroidogenic interstitial cell population. COUP-TFII promotes progenitor cell fate while suppressing Leydig cell differentiation. Moreover, embryonic deletion of COUP-TFII in mouse testes resulted in disorders of sex development, including reduced testicular size, Leydig cell hypoplasia, cryptorchidism, and hypospadias. Collectively, our findings highlight the critical role of COUP-TFII in orchestrating the transition from interstitial cells to Leydig cells during testicular development.

overall_design: Testes from E14.5 CD-1 (Charles River stock number 022) were separated from the mesonephros, snap-frozen, and stored at −80 °C. Two independent ChIP-seq experiments were performed by Active Motif, using 18 μg of sheared chromatin from 30 pooled embryonic testes and 5 μl of COUP-TFII antibody (Active motif, 61213). Libraries were sequenced by ActiveMotif as single-end 75-mers on an Illumina NextSeq 500 instrument.

middle: H

first: Martin

last: Estermann


title: Effect of Large Brown Adipocyte-secreted Proteins on Type 1 Diabetic Mice (NOD) Brown Adipose Tissue

city: St. Louis

first: Jeongmin

last: Lee

state: Missouri

address: 660 S. Euclid Ave

institute: Washington University in St. Louis

summary: Brown adipose tissue has been recognized as an important endocrine organ for metabolic health. In our study, we found that large proteins secreted by brown adipocyte (CB-100) promote the recovery of euglycemia in type 1 diabetic mice (NOD) when injected at an early stage of the disease. To further elucidate the in vivo effects of CB-100, we analyzed brown adipose tissue from both CB-100 and sham-treated mice. Differential gene expression analysis revealed that BAT from CB-100-treated NOD mice exhibited higher thermogenic activity. This suggests that the recovery of euglycemia in CB-100-treated mice may be attributed to enhanced thermogenic activity of the brown adipose tissue, which also contributes to glucose clearance

overall_design: NOD mice with blood glucose range between 190mg/dL and 230mg/dL were injected with CB-100 (>100kDa size fraction of brown adipocyte conditioned buffer) for 7 days (subcutaneous, 1.5mg/kg BW). After 2-8 weeks of post-injection, RNA was isolated from brown adipose tissue.


title: Temporal profiling of male cortical astrocyte transcription predicts molecular shifts from early development to aging

city: Blacksburg

first: Michelle

middle: Lynne

last: Olsen

state: VA

address: 970 Washington Street SW

department: School of Neuroscience

institute: Virginia Tech

summary: Astrocytes are the most abundant glial cell type in the central nervous system (CNS). Most astrocytes are born during the early postnatal period in the rodent brain and mature alongside neurons, demonstrating remarkable morphological structural complexity, attaining maturity in the second postnatal month. Across the remainder of the lifespan astrocytes participate in CNS homeostasis, support neuronal partners, and contribute to nearly all aspects of CNS functioning. In the present study, we analyzed astrocyte gene expression in rodent wild type cortex across the lifespan (7 days to 18 months).  A pairwise timepoint comparison of differential gene expression during early development and CNS maturation (7 days – 60 days) revealed four unique astrocyte gene clusters, each with hundreds of genes and demonstrating a unique temporal profile. These clusters distinctively related to cell division, cell morphology, Astrocytes are the most abundant glial cell type in the central nervous system (CNS). Astrocytes are born during the early postnatal period in the rodent brain and mature alongside neurons, demonstrate remarkable morphological structural complexity which is attained in the second postnatal month. Throughout this period of development and across the remainder of the lifespan, astrocytes participate in CNS homeostasis, support neuronal partners, and contribute to nearly all aspects of CNS function. In the present study, we analyzed astrocyte gene expression in the cortex of wild-type rodents throughout their lifespan (postnatal 7 days to 18 months). A pairwise timepoint comparison of differential gene expression during early development and CNS maturation (7 days–60 days) revealed four unique astrocyte gene clusters, each with hundreds of genes, and which demonstrate unique temporal profiles. These clusters are distinctively related to cell division, cell morphology, cellular communication and vascular structure and regulation. A similar analysis across adulthood and in the aging brain (3 months to 18 months) identified similar patterns of grouped gene expression related to cell metabolism and cell structure. Additionally, our analysis identified that during the aging process astrocytes demonstrate a bias toward shorter transcripts, with loss of longer genes related to synapse development and a significant increase in shorter transcripts related to immune regulation and the response to DNA damage. Our study highlights the critical role that astrocytes play in maintaining CNS function throughout life, and reveals molecular shifts that occur during development and aging.

overall_design: To investigate the gene expression difference in astrocyte development and aging process, we isolated astrocytes  from P7, P14, P21, P28, P60, 3m, 6m, 12m and 18m WT male mouse cortices with the magnetic cell isolation method. RNA was extracted to do RNA sequencing with the polyA enrichment method.

middle: L


title: Transfer RNA acetylation regulates in vivo mammalian stress signaling [tRNAseq]

status: Public on Mar 25 2025

city: Frederick

first: Colin

state: MD

department: RNA Biology Laboratory

institute: NCI

type: Non-coding RNA profiling by high throughput sequencing

summary: Transfer RNA (tRNA) modifications are crucial for protein synthesis, but their physiological roles remain poorly understood. Here we investigate the impact of N4-acetylcytidine (ac4C), a highly conserved tRNA modification, using a Thumpd1 knockout mouse model. We find that loss of Thumpd1-dependent tRNA acetylation leads to reduced levels of tRNALeu, increased ribosome stalling and collisions, and activation of eIF2α phosphorylation. Thumpd1 knockout mice exhibit growth defects and sterility. Remarkably, concurrent knockout of Thumpd1 and the stress-sensing kinase Gcn2 causes penetrant postnatal lethality, revealing a critical genetic interaction. Our findings demonstrate that a modification restricted to a single site within type II cytosolic tRNAs can regulate ribosome-mediated signaling in mammalian organisms. By providing insight into how tRNA modifications shape signaling and cell fate in response to stress, this work opens up novel strategies for therapeutic intervention and translational control.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: mim-tRNAseq

first: Roxane

last: Khoogar


title: Head and Embryo 80S monosomes are much more translationally active than 80S in other tissues

city: Leeds

first: LeedsOmics

last: UoLeeds

state: West Yorkshire

address: Clarendon Way

department: Cross-faculty

country: United Kingdom

institute: University of Leeds

summary: Translational regulation at the stage of initiation impacts the number of ribosomes translating each mRNA molecule. For example, multiple ribosomes can engage on a single mRNA forming a polysome, resulting in highly efficient protein synthesis. However, the translational activity of single 80S ribosomes on mRNA (monosomes) is less well understood, even though these 80S monosomes represent the dominant ribosomal complexes in many tissues. Here, we used cryo-EM to determine the translational activity of 80S monosomes across different tissues in Drosophila melanogaster. We discovered that while head and embryo 80S monosomes are highly translationally active, testis and ovary 80S monosomes are translationally inactive. RNA-Seq analysis of head monosome- and polysome-translated mRNAs, revealed that head 80S monosomes preferentially translate mRNAs with TOP motifs, short 5’-UTRs, short ORFs and are enriched for uORFs. Overall, these findings highlight that regulation of translation initiation, and therefore the number of ribosomes bound per mRNA, varies substantially across tissues.

overall_design: In order to investigate differential transcript enrichment in different ribosome fractions (80S vs Polysomes), we performed Frac-seq analysis on purified 80S and polysome fractions from the flies' heads in biological triplicates for each sample group. Total RNA-seq  from the heads was also performed as a control

first: Albert

last: Blandy

first: Tayah

last: Hopes

first: Elton

last: Vasconcelos

first: Amy

last: Turner

first: Bulat

last: Fatkhullin

first: Michaela

last: Agapiou

first: Juan

last: Fontana

first: Julie

last: Aspden


title: An ultraconserved snoRNA-like element in long noncoding RNA CRNDE promotes ribosome biogenesis and cell proliferation (CRISPRi screen) [A-498]

city: Dallas

first: Joshua

last: Mendell

state: TX

address: 6000 Harry Hines Blvd., NA6.200A

department: Molecular Biology

institute: UT Southwestern Medical Center

summary: Cancer cells frequently upregulate ribosome production to support tumorigenesis. While small nucleolar RNAs (snoRNAs) are critical for ribosome biogenesis, the roles of other classes of noncoding RNAs in this process remain largely unknown. Here we performed CRISPR screens to identify essential long noncoding RNAs (lncRNAs) in renal cell carcinoma (RCC) cells. This revealed that an alternatively-spliced isoform of lncRNA Colorectal Neoplasia Differentially Expressed containing an ultraconserved element (UCE), referred to as CRNDEUCE, is required for RCC cell proliferation. CRNDEUCE localizes to the nucleolus and promotes 60S ribosomal subunit biogenesis. The UCE of CRNDE functions as an unprocessed C/D box snoRNA that directly interacts with ribosomal RNA precursors. This facilitates delivery of eIF6, a key 60S biogenesis factor, which binds to CRNDEUCE through a sequence element adjacent to the UCE. These findings highlight the functional versatility of snoRNA sequences and expand the known mechanisms through which noncoding RNAs orchestrate ribosome biogenesis.

overall_design: A genome-wide CRISPRi screen was performed in A-498 cells expressing dCas9. Two independent clones were used for the screen. Samples were collected before (D0, control samples) and 19 days after prolonged growth (D19).

first: Jong-Sun

first: Tu

last: Dan

first: He

last: Zhang

middle: T


title: An ultraconserved snoRNA-like element in long noncoding RNA CRNDE promotes ribosome biogenesis and cell proliferation (CRISPRi screen) [ACHN]

overall_design: A genome-wide CRISPRi screen was performed in ACHN cells expressing dCas9. Two independent clones were used for the screen. Samples were collected before (D0, control samples) and 12 days after prologned growth (D12).


title: An ultraconserved snoRNA-like element in long noncoding RNA CRNDE promotes ribosome biogenesis and cell proliferation (CRISPRi screen) [786-O]

overall_design: A genome-wide CRISPRi screen was performed in 786-O cells expressing dCas9. Two independent clones were used for the screen. Samples were collected before (D0, control samples) and 15 days after prolonged growth (D15).


title: Effect of Large Brown Adipocyte-secreted Proteins on Type 1 Diabetic Mice (NOD) inguinal white adipose tissue

first: Jeongmin

summary: Brown adipose tissue has been recognized as an important endocrine organ for metabolic health. In our study, we found that large proteins secreted by brown adipocyte (CB-100) promote the recovery of euglycemia in type 1 diabetic mice (NOD) when injected at an early stage of the disease. To further elucidate the in vivo effects of CB-100, we analyzed brown adipose tissue from both CB-100 and sham-treated mice. Differential gene expression analysis revealed that CB-100 treatment promote the adipocyte proliferation and browning wihtin inguinal white adipose tissue. This suggests that the recovery of euglycemia in CB-100-treated mice may be attributed to the recovery of healty white fat and its browning, which also contributes to glucose clearance

overall_design: NOD mice with blood glucose range between 190mg/dL and 230mg/dL were injected with CB-100 (>100kDa size fraction of brown adipocyte conditioned buffer) for 7 days (subcutaneous, 1.5mg/kg BW). After 2-8 weeks of post-injection, RNA was isolated from inguinal white adipose tissue.


title: Cell-intrinsic metabolic phenotypes identified in glioblastoma patients using mass spectrometry imaging of 13C-labeled glucose metabolism

city: Cambridge

first: Ashley

middle: David

last: Sawle

address: Robinson Way

institute: Cancer Research UK Cambridge Institute

summary: Transcriptomic studies have attempted to classify glioblastoma (GB) into subtypes that predict survival and that have different therapeutic vulnerabilities.  Here we identified three metabolic subtypes: glycolytic, oxidative and a mixed glycolytic/oxidative by mass spectrometry imaging of rapidly excised tumour sections from two GB patients infused with [U-13C]glucose and from spatial transcriptomic analysis of contiguous sections.  The phenotypes did not correlate with microenvironmental features, including proliferation rate, immune cell infiltration, and vascularisation, were retained when patient-derived cells were grown in vitro, or as orthotopically implanted xenografts, and were robust to changes in oxygen concentration, demonstrating their cell intrinsic nature.  The spatial extent of the regions occupied by cells displaying these distinct metabolic phenotypes are large enough to be detected using clinically applicable metabolic imaging techniques.  A limitation of the study is that it is based on only two patient tumours, albeit on multiple sections, and therefore represents a proof-of-concept study. Glioblastoma is the most common primary adult brain cancer. Transcriptomic analyses have attempted to classify GB into subtypes that could predict treatment response, with a recent study that used a pathway-based classification defining metabolism-associated subtypes with distinct therapeutic vulnerabilities.  These included a mitochondrial subtype, which is associated with a more favourable clinical outcome and that is sensitive to inhibitors of oxidative phosphorylation, and a glycolytic/plurimetabolic subtype that is resistant to multiple treatment types. An important question is the extent to which the metabolism displayed by tumour cells in vivo are cell intrinsic and how much they are defined by the tumour microenvironment. We have addressed this question using mass spectrometry imaging of rapidly excised tumour sections from GB patients infused with [U-13C]glucose immediately prior to surgery to image tumour cell metabolic fluxes in vivo and from a spatial transcriptomic analysis of adjacent sections.  To our knowledge, this is the first report demonstrating high resolution imaging of metabolic fluxes in a human tumour in vivo.

overall_design: RNAseq profiling of glioblastoma derived neurospheres cultured under hypoxia and normoxia

first: Anastasia

last: Tsyben

first: Andreas

last: Dannhorn

first: Gregory

last: Hamm

first: Manthos

last: Pitoulias

first: Dominique-Laurent

last: Couturier

first: Mayen

last: Briggs

first: Alan

last: Wright

first: Cara

last: Brodie

first: Jodi

last: Miller

first: Eleanor

middle: C

last: Williams

first: Lovisa

last: Franzén

first: Grant

last: De Jong

first: Tannia

last: Gracia

first: Fani

last: Memi

first: Omer

last: Bayraktar

first: Ram

last: Adapa

first: Jyotsna

last: Rao

first: Ariadna

last: González-Fernández

first: Josephine

last: Bunch

first: Zoltan

last: Takats

first: Simon

last: Barry

first: Richard

last: Goodwin

last: Mair

first: Kevin

last: Brindle


title: Interleukin-34-dependent perivascular macrophages promote vascular function in the brain

status: Public on Mar 23 2025

city: Zurich

first: Hannah

middle: Jade

last: Van Hove

summary: The development of most macrophages depends on the colony-stimulating factor 1 (CSF-1) receptor, which has two ligands: CSF-1 and interleukin-34 (IL-34). While IL-34 is required for the homeostasis of microglia, the parenchymal macrophages in the central nervous system (CNS), it is unclear whether brain border-associated macrophages (BAMs) also depend on this cytokine. Here, we demonstrated that the embryonic development of murine BAMs in the choroid plexus, leptomeninges, and perivascular spaces required CSF-1, while IL-34 was critical for their maintenance in adulthood. In the brain, Il34 was expressed by mural cells and perivascular fibroblasts, and its transgenic deletion in these cells interrupted BAM maintenance. Il34-deficiency coincided with transcriptional changes in vascular cells, leading to increased flow velocity and vasomotion in pial and penetrating arterioles. Similarly, Mrc1CreCsf1rfl/fl mice lacking CD206+ perivascular BAMs exhibited increased hemodynamics in arterial networks. These findings reveal a crosstalk between vascular cells and CNS macrophages regulating cerebrovascular function.

overall_design: scRNA-seq of FACS-sorted mural cells (MCs) and fibroblasts (FBs) (CD13+ and/or CD140a+O4- cells), endothelial cells (ECs) (CD31+), astrocytes (AC) (ACSA-2+), BAMs (CD11bhiF4/80+) and microglia (CD11b+F4/80hi) from adult Mrc1CreCsf1rfl/fl and Csf1rfl/fl mice.


title: Impact of Tda1 on gene expression during glycerol cultivation in Saccharomyces cerevisiae

city: Nagoya-shi

first: Kazuki

last: Nonaka

address: Furo-cho

country: Japan

institute: Nagoya University

summary: The energy metabolism pathways are significantly influenced by the available carbon sources. In Saccharomyces cerevisiae, energy is primarily produced through aerobic respiration during glycerol cultivation, a process believed to depend on the yeast AMPK (AMP-activated protein kinase) homolog, Snf1. It has been reported that Snf1 increases the expression of respiratory genes by phosphorylating transcriptional activators in environments where glucose is unavailable. We discovered that Tda1, activated by Snf1, phosphorylates Hxk2. Hxk2 has been reported to function as a transcriptional repressor. Therefore, we analyzed how Tda1 affects the expression of respiratory genes by RNA-seq analysis of glycerol-cultured cells.

overall_design: RNA-seq profiling of BY4741 WT, tda1Δ, snf1Δ, and Hxk2-S15A mutant cells under glycerol culture conditions.

first: Kohei

last: Nishimura

first: Kazuma

last: Uesaka

first: Emi

last: Mishiro-Sato

first: Minako

last: Fukase

first: Rei

last: Kato

first: Fumihiko

last: Okumura

first: Kunio

last: Nakatsukasa

first: Keisuke

last: Obara

first: Takumi

last: Kamura


title: Gene expression profile at single cell level of mouse tibialis anterior muscle cells from young and aged mice treated with or without cardiotoxin (CTX)

city: Bunkyo-ku

first: Hiroyuki

last: Koike

state: Tokyo

address: 1-5-45 Yushima

department: Department of Medical Biochemistry

institute: Institute of Science Tokyo

summary: The findings show that skeletal muscle tissue during regeneration contains a variety of macrophage subpopulations, whose compositional proportions and functions change with age. Single-cell RNA sequencing (scRNA-seq) was used to analyse intercellular communication between proliferating skeletal muscle stem cells and macrophage subpopulations.

overall_design: Live (7AAD-negative) leukocytes (CD45-positive), Fibro-adipogenic progenitors (Ly6A/E-positive), endothelial cells (CD31-positive), and skeletal muscle stem cells (CD106-positive) were sorted from mouse anterior tibial muscle tissue on days 0 and 3 of regeneration by fluorescence-activated cell sorting (FACS) and processed for droplet-based scRNA-seq.

first: Ichiro

last: Manabe

first: Yumiko

last: Oishi


title: Iterative transcription factor screening enables rapid generation of microglia-like cells from human iPSC - TFiMGLs are responsive to disease-relevant stimuli

city: Boston

first: Songlei

last: Liu

state: MA

address: 77 Avenue Louis Pasteur

institute: Harvard University

summary: Differentiation of induced pluripotent stem cells (iPSCs) into specialized cell types is essential for uncovering cell-type specific molecular mechanisms and interrogating cellular function. Transcription factor (TF) screens have enabled efficient production of a few cell types; however, engineering cell types that require complex TF combinations remains challenging. Here, we report an iterative, high-throughput single-cell TF screening method that enables identification of TF combinations for specialized cell differentiation, which we validated by differentiating human microglia-like cells. We found that the expression of six TFs, SPI1, CEBPA, FLI1, MEF2C, CEBPB, and IRF8, is sufficient to differentiate human iPSC into cells with transcriptional and functional similarity to primary human microglia within 4 days.

overall_design: bulk RNA-seq of TFiMGLs (transcription factor induced microglial like cells) after treatment with either interferon gamma (IFNγ), beta amyloid (Aβ), or TDP-43

first: Liu

last: Songlei


title: Vesicles Secreted by Renal Cell Carcinoma Cells Cause Vascular Endothelial Cells to Express PSMA and Drive Tumor Progression

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

summary: Prostate-specific membrane antigen (PSMA) protein expression is induced during prostate cancer progression and metastasis. Recently, we reported that PSMA-positive vesicles released by prostate cancer cell lines enhanced vascular endo-thelial cell angiogenesis and that PSMA may be involved in tumor angiogenesis. Simi-larly, it is known that PSMA is upregulated in peritumoral vessels in renal cell carcinoma (RCC). In this study, we investigated the significance and molecular function of PSMA in RCC. PSMA immunohistochemical staining confirmed PSMA presence only in peri-nephric tumor vessels, and PSMA intensity was strongly correlated with recurrence rate and venous invasion. Spatial gene expression analysis revealed that FOLH1 expression, which codes PSMA, was upregulated in tumor blood vessels around renal cancer, and that angiogenesis-related pathways were enhanced. The 10,000 g pellet fraction of the renal cancer cell lines Caki1- and ACHN-conditioned medium   (CM) in-duced PSMA positivity in human umbilical vein endothelial cells (HUVECs) and en-hanced tube formation. Mass spectrometry indicated that the 10,000 g pellet fraction contained various kinds of growth factors, like GDF15 and MYDGF. RNA sequencing showed that supplementing HUVECs with RCC cell CM-enhanced angiogenesis-related signaling pathways. Conclusively, microvesicle components secreted by RCC cells transform vascular endothelial cells into PSMA-positive cells, enhancing angiogenesis.

overall_design: Visium HD (10x genomics) for Formalin-fixed, paraffin-embedded (FFPE) samples of resected prostate specimen

first: Ryuta

last: Watanabe

first: Tomohisa

last: Sakaue

first: Mie

last: Kurata

first: Riko

last: Kitazawa

first: Noriyoshi

last: Miura

first: Tadahiko

last: Kikugawa

first: Takashi

last: Saika


title: Iterative transcription factor screening enables rapid generation of microglia-like cells from human iPSC - Second round of pooled screening identified an initial set of TFs for inducing microglia gene expression.

overall_design: scRNA-seq of second pooled TF screening. Following the dual transfection of 42 TF vectors and SFC (SPI1-T2A-FLI1-P2A-CEBPA) casette into hiPSCs, cells were purified and treated with dox for 4 days. Tra-1-60 negative cells were sorted for scRNA-seq. For the second iteration, 5% stem cells and 5% MG3.1-SFC were spiked in as undifferentiated and initial differentiation control.


title: ETV2 Overexpression Promotes Efficient Differentiation of Pluripotent Stem Cells to Endothelial Cells

city: Madison

first: Yunfeng

last: Ding

state: WI

address: 1415 Engineering Dr

department: Chemical and Biological Engineering

institute: University of Wisconsin - Madison

summary: Directed differentiation of endothelial cells (ECs) from human pluripotent stem cells (hPSCs) typically takes around fourteen days, requires optimization of parameters such as hPSC seeding density and medium supplement concentration or timing, and often necessitates cell sorting to achieve high purity ECs. Overexpression of cell type-specific transcription factors in hPSCs has been shown to lead to efficient differentiation of many cell types, including neurons, astrocytes and hepatocytes. ETV2 has been identified as an essential transcription factor for endothelial cell fate commitment during development. Here, we present a simple, well-characterized differentiation method to generate ECs by overexpressing ETV2 in an inducible manner (iETV2) in hPSC cell lines. The result is a two-stage differentiation strategy, in which ECs are differentiated in a basal medium during stage I and then expanded in endothelial medium during stage II. By optimizing hPSC seeding density and differentiation medium, we generated an EC population with more than 99% pure CD31+ CD144+ cells without any cell sorting in just five days. In vitro angiogenesis potential of the iETV2-ECs was confirmed in cord formation assays and iETV2-EC uptake of acetylated LDL and response to inflammatory cytokines was confirmed. We compared transcriptomics of iETV2-ECs to the ECs generated from hPSCs via directed differentiation and confirmed similarity of gene expression profiles of ECs generated by these two different approaches. Furthermore, we found that iETV2-ECs respond to previously identified Wnt signaling agonist CHIR99021 and TGFβ signaling inhibitor RepSox to acquire aspects of brain EC phenotype. These findings underscore that iETV2-ECs can serve as easily scalable endothelial source, powering a variety of research applications, potentially including in vitro blood-brain barrier modeling.

overall_design: IMR90-4 iPSC line was edited to express ETV2 in an inducible manner. We differentiated iETV2-ECs by inducing ETV2 expression in this edited cell line. Media for differentiation and expansion was tested. We also differentiated ECs from unedited IMR90-4 iPSC line through mesiderm and endothelial progenitors.

first: Soniya

last: Tamhankar

first: Eric

middle: V

last: Shusta

first: Sean

middle: P

last: Palecek


title: Iterative transcription factor screening enables rapid generation of microglia-like cells from human iPSC - First round of pooled screening identified an initial set of TFs for inducing microglia gene expression.

overall_design: scRNA-seq of first pooled TF screening. Following transfection of 40 TF vectors into hiPSCs, cells were purified and treated with dox for 4 days. Tra-1-60 negative cells were sorted for scRNA-seq. For the first iteration, 10% of stem cells were spiked in as undifferentiated control.


title: Genome-Scale DNA Methylome and Transcriptome Profiles of Prostate Cancer Recurrence After Prostatectomy

city: Dunedin

first: Aniruddha

last: Chatterjee

state: Otago

address: 270 Great king Street

department: Pathology

country: New Zealand

institute: University of Otago

type: Methylation profiling by genome tiling array

summary: Prostate cancer (PCa) is a major health burden world-wide and despite early treatment, a very large proportion of patients present with biochemical recurrence (BCR) post-treatment, reflected by a rise in PSA over a clinical threshold. Novel transcriptomic and epigenomic biomarkers can provide a powerful tool for clinical management of PCa. Here we provide matched high-depth RNA-Sequencing and array-based genome-wide DNA methylome data of PCa patients (n = 17) with, or without, evidence of BCR following early radical prostatectomy. We have utilized Formalin-Fixed Paraffin-Embedded tissues to generate this data and included technical replicates to provide further validity of the data. We describe the sample features, experimental design, methods and bioinformatic pipeline for processing these multi-omic data. Importantly, we provide comprehensive clinical, histopathological, and follow-up data for each patient to enable correlating transcriptome and methylome features with clinical features. Our data will contribute towards the efforts of developing epigenomic and transcriptomic markers for BCR and also facilitate a deeper understanding of the molecular basis of PCa recurrence.

overall_design: Herein we aimed to generate the methylomic and transcriptomic profiles of PCa patients with, or without, evidence of BCR following early radical prostatectomy. DNA and RNA was extracted from FFPE tissues from a cohort of 17 radical prostatectomy patients.  We have generated matched, high-depth, genome-scale profiles of the DNA methylome (MethylationEPIC v2.0 array) and RNA transcriptome (RNA-Seq). Six samples showed a mean detection p-value >0.05 and hence were not considered for MethylationEPIC v2.0 array analysis. Additionally, we have also added technical replicates for methylome and RNA-Seq samples for assessing reproducibility.

first: Jim

last: Smith

first: Euan

last: Rodger

first: Priyadarshana

last: Ajithkumar


title: The anti-androgenic fungicide triticonazole induces region-specific transcriptional changes in the developing rat perineum and phallus

city: Rennes

first: Frédéric

last: Chalmel

state: France

address: 9 avenue du Pr. Léon Bernard

department: Physiology and physiopathology of the urogenital tract

country: France

institute: Inserm U1085-Irset

summary: Intrauterine exposure to endocrine disrupting chemicals can interfere with male reproductive development. This can lead to male reproductive disorders such as hypospadias, cryptorchidism and reduced fertility, as well as shorter anogenital distance (AGD) – a biomarker for incomplete androgen-dependent fetal masculinization. However, it remains challenging to predict adverse in vivo outcomes based on in vitro effect patterns for many chemicals. This is a challenge for modern toxicology, which aims to reduce animal testing for chemical safety assessments. To enable the transition towards higher reliance on alternative test methods, we need to better map underlying mechanisms leading to adverse effects. Herein, we have analyzed the transcriptome of the perineum and phallus of male fetal rats and defined the impacts of exposure to an anti-androgenic fungicide, triticonazole. Previously we have shown that developmental exposure to triticonazole can induce short male AGD, but without a marked effect on the transcriptome of the fetal testes. In contrast, we report here significant changes to the transcriptional landscape of the perineum and phallus, including regional differences between these adjacent tissues. This highlights the importance of analyzing the correct tissue when characterizing mechanisms of complex in vivo effect outcomes. Our results provide a rich resource for the spatiotemporal gene networks that are involved in the development of male external genitalia, and that can be disrupted upon exposure to chemicals that prevent normal masculinization of the perineum and phallus. Such data will be critical in the development of novel alternative test methods to determine the endocrine disrupting potential of existing and emerging chemicals.

overall_design: Testicular mRNA profiles of male fetal rats at gestational day 17 or 21 exposed to triticonazole during gestation (from day 7-21) were generated by Bulk RNA Barcoding and sequencing (BRB-seq).

first: Monica

last: Kam Draskau

first: Camilla

last: Lindgren Schwartz

first: Bertrand

last: Evrard

first: Aurélie

last: Lardenois

first: Andrew

last: Pask

first: Terje

last: Svingen


title: Iterative transcription factor screening enables rapid generation of microglia-like cells from human iPSC - Timelapse sequencing data of Transcription Factor induced Microglia Like cells

first: Songlei

last: Liu

overall_design: bulk RNA-seq of TFiMGLs (6 transcription factor induced microglial like cells) over time (days 0, 1, 2, 3, 4, and 6).

first: Liu

last: Songlei


title: Mtc91 - H3K27me3 ChIPmentation of activated murine CD8+ T-cells cultured in high (0.625 mg/mL holotransferrin) or low iron (0.001 mg/mL holotransferrin) conditions

status: Public on Mar 22 2025

city: Oxford

first: Megan

middle: Rhonwen

last: Teh

address: John Radcliffe Hospital, Headley Way

department: MRC Weatherall Institute of Molecular Medicine

institute: University of Oxford

summary: Iron is an irreplaceable co-factor for metabolism and iron deficiency affects >1 billion people, causing anaemia and impairing immunity. How iron deprivation influences normal cellular function remains poorly characterised. In activated CD8+ T-cells we found that iron scarcity profoundly stalled proliferation and disrupted mitochondrial redox control without influencing cell viability. The TCA cycle was partially redirected to a reductive trajectory, and the repressive H3K27me3 histone mark, usually decreased post-activation, was maintained. Surprisingly, aspartate, which is crucial for proliferation, was increased in stalled iron deficient cells but was not utilised cytosolically, indicating trapping within depolarised mitochondria. Exogenous aspartate increased ATP, suppressed H3K27me3 and markedly rescued clonal expansion. We propose that iron scarcity creates a metabolic bottleneck impairing activation and proliferation of T-cells, and which is bypassed by resupplying biochemical processes with aspartate. These findings reveal mechanistic consequences of iron deficiency and shed light on the response of T-cells to nutritional variation.

overall_design: To identify how iron deficiency impacts chromatin marks in activated murine CD8+ T-cells we completed ChIPmentation for H3K27me3 on activated murine CD8+ T-cells cultured in either high iron (0.625 mg/mL holotransferrin) or low iron (0.001 mg/mL holotransferrin) for 2 days.  CD8+ T-cells derived from 1 mouse were split across the 2 iron conditions.  Cells from each iron condition were pulled down with antibodies for H3K27me3.

first: Teh

last: Megan Rhonwen

first: Drakesmith

last: Hal


title: CD37 Regulates the Self-Renewal of Leukemic Stem Cells via Integrin Mediated Signaling in Acute Myeloid Leukemia

city: Shanghai

first: Lu

last: Jinyuan

address: 389 Xincun Rd.

institute: Tongji Hospital

summary: Leukemic stem cells (LSCs) are a small subset of leukemia cells which drive leukemia initiation and maintenance. Herein, we report that CD37, a member of transmembrane 4 superfamily (TM4SF), regulates the survival of acute myeloid leukemia (AML) cells as well as the self-renewal of AML LSCs. The downregulation of CD37 retarded proliferation and increased apoptosis in human AML cell lines THP-1 and OCI-AML2. Deficiency of CD37 in vivo had a minimal effect on normal hematopoiesis, but significantly impeded leukemia maintenance and propagation, which led to increased apoptosis and decreased cell cycle entry in AML blasts as well as impaired colony formation and declined frequency of AML LSCs in the serial transplantation. Furthermore, CD37 interacted with integrin α4β7 and activated PI3K-AKT pathway mediated by integrin signaling. Our study provides novel insights for targeted therapy of AML, indicating CD37 as a safe and effective target for immunotherapy.

overall_design: RNA-seq profiling of CD37 fl/fl and CD37 -/- bone marrow YFP+,c-kit+ LSCs obtained from the secondary transplantation of MLL-AF9 AML mice model at week 6. Each genotype has 2 independent replicates.

first: Jinyuan

last: Lu

first: Lixin

last: Lv

first: Xiaoxue

last: Tian

first: Zheng

last: Li

first: Yuting

last: Ma

first: Nannan

first: Jian

last: Wang

first: Guangming

first: Yu

last: Zeng

first: Wenjun

last: Zhang

first: Jun

last: Xu

first: Aibin

last: Liang


title: SWI/SNF complex-mediated ZNF410 cooperative binding maintains chromatin accessibility and enhancer activity [ATAC-Seq]

first: Siyuan

address: No.131, Dongan Road, Shanghai

institute: Fudan Unversity

summary: Clustering of multiple transcription factor binding sites (TFBSs) for the same TF has proved to be a pervasive feature of cis-regulatory elements in eukaryotic genome. However, contribution of binding sites within the homotypic clusters of TFBSs (HCTs) to TF binding and target gene expression remains to be understood. Here, we characterize the CHD4 enhancers that harbor unique functional ZNF410 HCTs genome-wide. We uncover that ZNF410 controls chromatin accessibility and activity of the CHD4 enhancer regions. We demonstrate that ZNF410 binds to the HCTs in a collaborative fashion, further conferring transcriptional activation. Especially, three ZNF410 motifs (sub-HCTs) located at 3´ end of the distal enhancer act as “switch motifs” to control the chromatin accessibility and enhancer activity. Mechanistically, SWI/SNF complex is selectively required to mediate cooperative ZNF410 binding for CHD4 expression. Together, our findings expose a complex functional hierarchy of homotypic clustered motifs, which cooperates to fine-tune target gene expression.

overall_design: To explore the changes of chromatin accessibility upon ZNF410 KO or binding motif mutation, we performed assay for transposase accessible chromatin with high-throughput sequencing (ATAC-seq) experiments in K562 cells.

first: S

first: X

last: Lan


title: KDM4C inhibition blocks tumor growth in basal breast cancer by promoting cathepsin L-mediated histone H3 cleavage

first: Kornelia

last: Polyak

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: Triple-negative breast cancer (TNBC) is a highly aggressive disease with inferior prognosis necessitating the discovery of novel actionable targets. Here, we show that KDM4C, a histone demethylase amplified in a subset of TNBC, is a driver of TNBC tumor growth. Integrative multi-omic analysis demonstrated that KDM4C inhibition triggers chromatin and transcriptomic remodeling without substantial changes of its canonical substrates H3K9me3 and H3K36me3. Rather KDM4C loss caused proteolytic cleavage of histone H3 mediated by cathepsin L (CTSL) recruited to the chromatin by GRHL2. Metabolomic profiling showed reduced glutathione levels following KDM4C inhibition partly due to a decrease in glutamate-cysteine ligase (GCLC) caused by CTSL-mediated histone H3 cleavage and led to increased reactive oxygen species. The expression of KDM4C and GCLC correlated in TNBC and combined targeting of KDM4C and the GSH axis improved response to cisplatin in TNBC. Our study reveals a novel, non-canonical role for KDM4C in TNBC that links metabolic and epigenetic profiles.

overall_design: We generated the Dox-inducible KDM4C shRNA knockdown celll models based on KDM4C amplified basal breast cancer cell line HCC1954 and SUM149, as well as KDM4C non-amplified cell line T47D. We performed RNA-seq, ATAC-seq, H3K9me3/H3K36me3/H3K4me3/KDM4C ChIP-seq under treatments of DMSO, 0.1ug/ml doxycycline and 10 ?M ML324 or 1 uM QC6352 (KDM4 family small molecule inhibitors). Furthermore, we also generated ML324 resistant HCC1954 and SUM149 cell lines and perfromed RNA-seq. Next, since we identified cathepsin L (CTSL) as a endopeptidase mediating histone H3 N ternminal tail clipping and GRHL2 as it's chromatin recruiter, we generated CTSL and GRHL2 CRISPR KO cell models and did CTSL and GRHL2 ChIP-seq on them in the presentce of 10 uM ML324.

first: Li

last: Zheqi

first: Peluffo

last: Guillermo

first: Polyak

last: Kornelia


title: Cyclic GMP-AMP Synthase (cGAS) Deletion Promotes Less Prominent Inflammatory Macrophages and Sepsis Severity in Catheter-Induced Infection and LPS Injection Models

city: Worcester

first: Patipark

last: Kueanjinda

address: 368 Plantation St

institute: University of Massachusetts Medical School

summary: Activation of cGAS, a cytosolic receptor recognizing double-stranded DNA, in macrophages is important in sepsis (a life-threatening condition caused by infection). The responses against sepsis induced by subcutaneous implantation of the Pseudomonas-contaminated catheters in cGAS-deficient (cGAS−/−) mice were lower than in wild-type (WT) mice as indicated by liver enzymes, white blood cell count, cytokines, and M1-polarized macrophages in the spleens. Likewise, a lethal dose of lipopolysaccharide (LPS) induced less severe sepsis severity as determined by mortality, organ injury, cell-free DNA, and serum cytokines. Patterns of the transcriptome of lipopolysaccharide (LPS)-stimulated bone marrow-derived macrophages were clearly different between cGAS−/− and WT cells. Gene set enrichment analysis (GSEA; a computational statistical determination of the gene set) indicated more prominent enrichment of oxidative phosphorylation (OXPHOS; the mitochondrial function) and mTORC1 pathways in LPS-activated cGAS−/− macrophages compared with WT. Meanwhile, LPS upregulated cGAS and increased cGAMP (a cGAS inducer) only in WT macrophages along with less severe inflammation in cGAS−/− macrophages, as indicated by supernatant cytokines, pro-inflammatory molecules (nuclear factor kappa B; NF-κB), M1 polarization (IL-1β, CD80, and CD86), and macrophage extracellular traps (METs; web-like structures composed of DNA, histones, and other proteins) through the detection of citrullinated histone 3 (CitH3) in supernatant and immunofluorescent visualization. In conclusion, less prominent pro-inflammatory responses of cGAS−/− macrophages than WT were demonstrated in mice (catheter-induced sepsis and LPS injection model) and in vitro (transcriptomic analysis, macrophage polarization, and METs).

overall_design: Comparative gene expression profiling analysis of RNA-seq data for BMDMs from cGAS KO in C57B/L6 backgroud mice after treatment with or without LPS for 1 h. RNA-seq was performed using Illumina NextSeq 500 sequencer.

first: Chatsuree

last: Suksamai

first: Warerat

last: Kaewduangduen

first: Pornpimol

last: Phuengmaung

first: Kritsanawan

last: Sae-Khow

first: Awirut

last: Charoensappakit

first: Suwasin

last: Udomkarnjananun

first: Sutada

last: Lotinun

first: Asada

last: Leelahavanichkul


title: SWI/SNF complex-mediated ZNF410 cooperative binding maintains chromatin accessibility and enhancer activity [ChIP-Seq]

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChlP-seq) for ZNF410 as well as the histone modifications H3K27ac, H3K4me3, and H3K9me3 in K562 cells.


title: Hypoxia and lactate influence VOC production in A549 lung cancer cells

city: Yokohama

first: Takeshi

last: Furuhashi

state: Kanagawa

address: 5th Floor Technocising Building, 2-6-3, Chojyamachi, Naka Ward

institute: ASM

summary: Investigating certain gene expressions in the VOC pathway and in lactate signaling, parallel to VOC production.

overall_design: RNAseq was conducted to find out transcriptional change related to VOC increase under hypoxia, glucose change as well as lactate addition.

first: Yuki

last: Matsumoto

first: Ryuga

last: Ishii

first: Takehito

last: Sugasawa

first: Shigenori

last: Ota


title: RNA-seq of activated murine CD8+ T-cells cultured in high (0.625 mg/mL holotransferrin) or low iron (0.001 mg/mL holotransferrin) conditions with or without 40 mM aspartate

first: Megan

last: Teh

overall_design: To identify how aspartate supplementation interacts with iron deficiency we sequenced activated murine CD8+ T-cells cultured in either high iron (0.625 mg/mL holotransferrin) or low iron (0.001 mg/mL holotransferrin) with or without 40 mM aspartate for 2 days.  CD8+ T-cells derived from 3 mice were each split across the 4 conditions (3 biological replicates matched across conditions).

first: Hal

last: Drakesmith


title: ZCCHC17 modulates neuronal RNA splicing and supports cognitive resilience in Alzheimer’s disease

city: New York

first: Andrew

last: Teich

state: NY

institute: Columbia University Irving Medical Center

summary: ZCCHC17 is a zinc-finger protein previously identified as a regulator of synaptic gene expression which becomes dysfunctional in Alzheimer’s disease. Here, we further investigate the function of ZCCHC17. Co-immunoprecipitation of ZCCHC17 followed by mass spectrometry analysis in human iPSC-derived neurons reveals that ZCCHC17’s binding partners are enriched for RNA splicing proteins. ZCCHC17 knockdown results in widespread RNA splicing changes that significantly overlap with splicing changes found in AD brain tissue, with synaptic genes commonly affected. ZCCHC17 expression positively correlates with cognitive resilience in AD patients, and we uncover an APOE4-dependent negative correlation of ZCCHC17 expression with tangle burden.  Furthermore, a majority of ZCCHC17 interactors also co-IP with known tau interactors, and we find significant overlap between alternatively spliced genes in ZCCHC17 knockdown and tau overexpression neurons.  These results demonstrate ZCCHC17’s role in neuronal RNA processing and its interactions with pathology and cognitive resilience in AD.

overall_design: 6 negative control siRNA-treated iPSC-derived neurons (siNC); 6 ZCCHC17 siRNA-treated iPSC-derived neurons (siZCC)

first: Anne

last: Bartosch

first: Elliot

last: Youth

middle: A

last: Sproul


title: Guard cell and whole plant expression of Arabidopsis thaliana TOR

status: Public on Mar 21 2025

city: Saskatoon

first: Peng

last: Gao

state: Saskatchewan

address: 107 Science Place

country: Canada

institute: Agriculture and Agri-Food Canada

summary: Water use efficiency has long been considered as an important target for the breeding of improved plant performance under drought. Minimizing leaf transpirational water loss via reduction of stomatal water conductance plays a key contributory role in drought resistance. In this study, we employed both guard cell (GC) targeted and constitutive ectopic overexpression of the Target of Rapamycin (TOR) kinase, a master regulator of multiple signaling networks in transgenic Arabidopsis thaliana, to investigate the impact of these expressed AtTOR transgenes in response to drought and water use efficiency. We performed genome-wide transcriptome analysis employing RNA-seq on the three Arabidopsis genotypes grown on the three water treatments, and further analysis will be used to elucidate the potential mechanism(s) contributing to differences in leaf stomatal physiology between WT and transgenic lines.

overall_design: We investigate the transcriptome of 27 samples from the three treatments (well-watered, drought-treated and re-watered) of the three genotypes (WT, GC, OE), with three replicates for each condition and genotype.

first: Raju

last: Datla

first: Leon

last: Kochian


title: ChIP-seq of activated murine CD8+ T-cells cultured in high (0.625 mg/mL holotransferrin) or low iron (0.001 mg/mL holotransferrin) conditions

overall_design: To identify how iron deficiency impacts chromatin marks in activated murine CD8+ T-cells we completed ChIPmentation for H3K27ac and H3K4me3 on activated murine CD8+ T-cells cultured in either high iron (0.625 mg/mL holotransferrin) or low iron (0.001 mg/mL holotransferrin) for 2 days.  CD8+ T-cells derived from 1 mouse were split across the 2 iron conditions.  Cells from each iron condition were split into 2 for pulldown with antibodies for either H3K27ac or H3K4me3


title: SWI/SNF complex-mediated ZNF410 cooperative binding maintains chromatin accessibility and enhancer activity [RNA-Seq]

first: Siyuan

last: Xu

overall_design: To investigate the function of ZNF410 in regulating gene expression, we established ZNF410 KO cell lines and performed RNA-seq experiments.

first: S

first: X

last: Lan


title: Pre-existing epigenetic state and differential NF-kB activation shape type 2 immune cell responses

city: NEW YORK

first: Sankar

last: Ghosh

department: Microbiology & Immunology

institute: Columbia University

summary: CD4+ T helper 2 (Th2) cells and their innate counterpart, group 2 innate lymphoid cells (ILC2s), drive type 2 immune responses, which protect against helminth infection and induce allergic inflammation. Although both cell types express an overlapping set of effector molecules, the identity of key transcription factors and how they differentially regulate gene expression in each cell type has not been determined. Here, we demonstrate that the transcription factor NF-kB is induced upon stimulation by the alarmin IL-33 in ILC2s and by TCR engagement in Th2 cells, yet NF-kB is essential for the function and expression of type 2 cytokines in ILC2s but not in Th2 cells. In ILC2s, the regulatory regions of key type 2 genes exist in an open chromatin conformation, which can be rapidly occupied by NF-kB following IL-33 stimulation. However, the same regulatory regions are less accessible in unstimulated Th2 cells, and other TCR-induced transcription factors such as NFAT play a more important role in regulating type 2 cytokine expression in Th2 cells. Thus, our results demonstrate a critical role of NF-kB in modulating type 2 immunity in a cell type-specific manner and reveal a remarkable plasticity of innate and adaptive lymphocytes in the use of pre-existing epigenetic states to differentially regulate the same set of effector genes.

overall_design: Integrated analysis of epigenome and transcriptome data from type 2 innate lymphoid cells and their adaptive counterpart, CD4+ T helper 2 cells.

first: Vincent

last: Guichard

first: Felipe

middle: B

last: Leao

first: Jingyao

last: Zhao

first: Yingyu

last: Zhang

first: Takamasa

last: Ito

first: Simon

last: Shirley

first: Thomas

middle: S

last: Postler

first: Ruxiao

last: Tian

first: Yuefeng

last: Huang


title: RNA-seq of naïve and activated murine CD8+ T-cells cultured in high iron (0.625 mg/mL holotransferrin) or low iron (0.001 mg/mL holotransferrin) conditions

first: Megan

last: Teh

overall_design: To identify how iron deficiency impacts activated murine CD8+ T-cell gene expression we sequenced naïve CD8+ T-cells isolated at day 0 and activated CD8+ T-cells cultured in either high iron (0.625 mg/mL holotransferrin) or low iron (0.001 mg/mL holotransferrin) for 2 days.  CD8+ T-cells derived from 3 mice were each split across the 3 conditions (3 biological replicates matched across conditions).

first: Hal

last: Drakesmith


title: Meningeal lymphatics-microglia axis regulates synaptic physiology [egfp/vegfc]

city: St. Louis

first: Jonathan

last: Kipnis

state: MO

address: 4515 McKinley Ave

institute: Washington University in St. Louis

summary: Microglia are thought to originate exclusively from primitive macrophage progenitors in the yolk sac (YS) and persist throughout life without contributions from definitive hematopoiesis. Here, using Ms4a3-Cre lineage tracing, pharmacological manipulation, and RNA-sequencing, we elucidated the presence and unique features of monocyte-derived macrophages (MDMs) in the brain parenchyma at baseline and during microglia repopulation. Using parabiosis and skull transplantation, we show that MDMs derived from both peripheral blood and skull bone marrow can repopulate microglia-depleted brains, and they display distinct transcriptional profiles compared to YS-derived microglia. Blood-derived macrophages possess a disease-associated microglia (DAM)-like phenotype, while skull-derived macrophages mirror injury-responsive microglia (IRM) and exhibit significant interactions with T cells. Repetitive microglia depletion and subsequent MDM engraftment in 5xFAD mice led to increased amyloid burden, suggesting differential responses of resident microglia and MDMs towards amyloid pathology. Our results reveal the heterogeneous origins and functions of microglia during cell turnover and neurodegeneration, offering insights that may guide microglia-targeted immunomodulatory strategies for neurological disorders.

overall_design: The subject AAV1-CMV-EGFP/VEGF-C-administrated 19-mo C57BL/6NCrL mice were cardio-perfused with 30 ml of 5 U/ml Heparin-PBS after 4-weeks from i.c.m. administration of AAV. Brains were harvested, located in heparin-PBS andcortices were dissected from 2 and 3 mice, respectively. Pulled Brains are minced with the sharp razor in RPMI 1640 medium with 2% FBS and digested by collagenase VIII and DNase (in 5 ml RPMI 1640 + 2 % FBS) for 45 minutes and titrated with P1000 pipettes once at 30 minutes after digestion starts, and one more at 45 minutes after.  Samples were strained through a 70-um strainer, and 5 ml RPMI 1640 + 10% FBS medium was added to stop digestion and spun down in 450g for 5 minutes. Pellets were resuspended in 14% BSA and spun down in 800 g for 10 minutes with slow acceleration/declaration. Supernatnace was removed carefully, and the pellet was resuspended in MACS buffer (0.5% BSA, 2 mM EDTA containing PBS), followed by spinning down (450g, 5 mins). 50 ul of CD45-bead (Miltenyi, 130-052-301) was added with 450 ul MACS buffer, and CD45+ cells were prepared according to the manufacturer's protocol.

first: Kyungdeok

last: Kim

first: Daviti

last: Abramishvili

first: Siling

last: Du

first: Zachary

last: Papadopoulos

first: Jay

last: Cao

first: Igor

last: Smirnov

first: Jean-Leon

last: Thomas

first: Marco

last: Colonna


title: Iterative transcription factor screening enables rapid generation of microglia-like cells from human iPSC -Single cell transcriptome timecourse analysis of TFiMGLs after SCF-MCI  (SPI1, FLI1, CEBPA, CEBPB, IRF8, and Mef2C) induction.

first: Songlei

last: Liu

summary: Transcription factor (TF) screens have enabled efficient production of a few cell types; however, engineering cell types that require complex TF combinations remains challenging. Here, we report an iterative, high-throughput single-cell TF screening method that enables identification of TF combinations for specialized cell differentiation, which we validated by differentiating human microglia-like cells. We found that the expression of six TFs, SPI1, CEBPA, FLI1, MEF2C, CEBPB, and IRF8, is sufficient to differentiate human iPSC into cells with transcriptional and functional similarity to primary human microglia within 4 days.

overall_design: We conducted a time course study to assess transcriptional profiles of hiPSC derived TFiMGLs under two different cell culture conditions. In the first condition, TFiMGLs were induced following the conditions of the transcription factor screen – in short, cells were continuously cultured in mTeSR Plus (+MT) media supplemented with Dox for 6 days. Whereas in the second condition, mTeSR Plus media was switched on day 2 to commercially available microglia-specific media (+MG) supplemented with Dox until day 6. Cells grown in both conditions were collected at days 2, 4, and 6 post-induction for scRNA-seq.

first: Mariana

last: Garcia-Corral

first: Patrick

last: Fortuna


title: Zinc eluted from glassware is a risk factor for embryo development in human and animal assisted reproduction

city: Kashihara

first: Hisato

last: Kobayashi

state: Nara

address: 840 Shijo-Cho

department: Department of Embryology

institute: Nara Medical University

summary: In assisted reproduction, many factors in the culture environment, including light, temperature, pH, and culture media, can reduce preimplantation embryo viability. Laboratory glassware is also a known risk factor for in vitro embryos; however, the underlying mechanisms that disrupt embryonic development remain unclear. We identified Zn eluted from glassware as an embryotoxic substance. In mouse embryos, Zn-induced delayed development, abnormalities in chromosome segregation, cytokinesis, zygotic gene activation (e.g., Zscan4c and murine endogenous retrovirus with leucine, also known as MERVL), and aberrantly upregulated developmental gene expression (e.g., Hoxa1, Hoxb9, T, and Fgf8) that could be mediated through metal regulatory transcription factors (e.g., Mtf1). Subsequently, Zn exposure led to significantly reduced blastocyst formation. Postimplantation, Zn-exposed embryos were associated with normal birth rates, however, the birth weight increased by an average of 18% compared with embryos cultured without Zn. Furthermore, Zn exposure affected the development of bovine and human embryos, with species-based variation in the strength and timing of these effects. To mitigate these embryotoxic effects, we identified a method to prevent glass toxicity using chelating agents. This research not only highlights the importance of risk control in embryo culture but also facilitates the development of safe and effective methods for assisted reproduction.

overall_design: Gene expression analysis of preimplantation embryos exposed with zinc metal ion in vitro.

first: Kazuo

last: Yamagata

first: Kazuki

last: Kurimoto

first: Tatsuma

last: Yao

first: Hiroki

last: Ikeda


title: A Metabolite-Based Resistance Mechanism Against Malaria

city: Oeiras

first: Miguel

last: Soares

address: Rua da Quinta Grande, 6

country: Portugal

institute: Instituto Gulbenkian de Ciência

summary: Severe presentations of malaria, arising from Plasmodium spp. infection, are often associated with accumulation of circulating bilirubin, a condition known as hyperbilirubinemia or jaundice of malaria. Whether this represents an adaptive or maladaptive response to Plasmodium spp. infection is not understood. Departing from the textbook view of hyperbilirubinemia reflecting a failure to excrete bilirubin, we demonstrate that bilirubin production by biliverdin reductase A (BLVRA) partakes in a host adaptive response to malaria. Genetic Blvra deletion exacerbated malaria mortality in mice; This was associated with a >10-fold increase in parasite burden, compared to control mice expressing BLVRA, which cleared the parasite and survived malaria. At concentrations in the range of jaundice of malaria, unconjugated bilirubin arrested the proliferation and killed asexual blood stages of the human-infective P. falciparum in vitro. This was associated with disruption of the parasite’s mitochondrion and food vacuole as well as with the accumulation of hemozoin in the parasite’s cytoplasm. Moreover, bilirubin inhibited hemozoin (β-hematin) synthesis in vitro, a vital heme-detoxifying pathway targeted by Quinoline-based antimalarial drugs such as chloroquine. In conclusion, hyperbilirubinemia represents an evolutionary conserved metabolite-based resistance mechanism against malaria.

overall_design: Mouse response to the infection of Plasmodium chabaudi chabaudi AS (Pcc AS) in Blvra+/+ wild-type and Blvra-/- knockout genotypes. Briefly, Blvra+/+ and Blvra-/- mouse blood samples were collected after 7 days of infection (i.e., peak of infection) and infected red blood samples were sorted. Sequencing reads were mapped against the Pcc AS genome.

first: Ana

last: Figueiredo

first: Fátima

last: Nogueira

first: Katherine

last: De Villiers

first: António

middle: G

last: de Sousa

first: Cäcilie

last: von Wedel

first: Pinkus

last: Tober-Lau

first: Susana

last: Ramos

first: Elisa

last: Jentho

first: Erin

last: Tranfield

first: Jessica

last: Thibaud

first: Denise

last: Duarte

last: Sousa

first: Sandra

middle: N

last: Pinto

first: Sonia

last: Trikha

first: Jamil

last: Kitoko

first: Lasse

last: Novel

first: Ghyslain

last: Mombo-Ngoma

first: Johannes

last: Mischlinger

first: Sini

last: Junttila

first: Piter

middle: J

last: Bosma

first: Silvia

last: Portugal

first: Florian

last: Kurth

first: Laura

last: Elo

first: Bindu

last: Paul

first: Rui

last: Martins


title: Altered Ten Eleven Translocation Methylcytosine Dioxygenase Expression and DNA Hydroxymethylation in a Mouse Model of Prostate Cancer [RNA-seq]

city: Springfield

first: Shannon

last: Kinney

address: 1215 Wilbraham Road Center for Sciences and Pharmacy

department: Pharmaceutical and Administrative Sciences

institute: Western New England University

summary: Background: DNA hydroxymethylation (5hmC) is known to be altered in human prostate cancer. An animal model is required to study the functional roles of the Ten Eleven Translocation (TET) DNA dioxygenases and the 5hmC modification in prostate cancer development and progression.  Methods: We characterized Tet expression, global genomic 5hmC, and genome-wide 5hmC patterns, and the transcriptome, in the Transgenic Adenocarcinoma of Mouse Prostate (TRAMP) autochthonous model of prostate cancer. Results: We observed increased mRNA and protein expression of Tet1 in TRAMP samples, as compared to normal mouse prostate. Additionally, we found minimal expression of Tet2 mRNA overall, and Tet3 mRNA levels appeared similar in both sample types.  However, TRAMP tumors expressed what appeared to be the inactive form of Tet3, versus the active form expressed in normal prostates. TRAMP tumors displayed global genomic hypohydroxymethylation (i.e., loss of 5hmC), and genome-wide analysis revealed widespread hypohydroxymethylation was interspersed with regions of locus specific hyperhydroxymethylation (i.e., increased 5hmC). The differentially hydroxymethylated regions correlated with altered gene expression, and pathway analyses indicated that these genes often participate in oncogenic pathways.Conclusions: Tet expression and 5hmC patterns are altered in the TRAMP model and closely match what has been observed in human prostate cancer, suggesting that TRAMP is a suitable model to study the role of Tets and 5hmC in prostate cancer development and progression.

overall_design: RNA from 2 normal mouse prostates and 2 TRAMP tumor samples were utilized for RNA-seq analysis.

first: Matthew

last: Aguilera

first: David

last: Klinkebiel

first: Victoryn

last: Williams

first: Jeffrey

last: Rovatti

first: Benjamin

last: Purizhansky

first: Barbara

last: Foster

first: Adam

middle: R

last: Karpf

middle: M


title: Aberrant ERK signaling in astrocytes impairs learning and memory in RASopathy-associated BRAF mutant mouse models [mouse_BRAF K499E]

city: Seongbuk-gu, Seoul

first: Seoyeon

last: Kim

address: 145, Anam-ro

country: South Korea

institute: Korea University

summary: Performed transcriptomic analysis of BRAF K499E-transfected astrocytes to investigate the molecular basis of BRAF K499E-induced learning and memory deficits.

overall_design: 3 BRAF K499E-transfected astrocyte were compared to 3 non-transfected controls.

first: Minkyung

last: Kang

first: Yong-Seok

last: Lee

first: Soowhee

first: Joon-Yong

last: An


title: Altered Ten Eleven Translocation Methylcytosine Dioxygenase Expression and DNA Hydroxymethylation in a Mouse Model of Prostate Cancer [hMeDIP-seq]

type: Methylation profiling by high throughput sequencing

overall_design: Genomic DNA from 2 normal mouse prostates and 2 TRAMP tumor samples were utilized for hMeDIP-seq analysis to characterize differences in 5hmC patterns across the genomes of the two sample types.


title: Distinct routes of clonal progression in SF3B1-mutant myelodysplastic syndromes

city: Pavia

first: Martina

last: Sarchi

address: Via Ferrata 9

department: Dept. of Molecular Medicine

country: Italy

institute: University of Pavia

summary: Myelodysplastic syndromes (MDS) are clonal stem cell disorders driven by heterogeneous genetic alterations leading to variable clinical course. MDS with splicing factor SF3B1 mutations is a distinct subtype with a favorable outcome. However, selected co-mutations induce poor prognosis and how these genetic lesions cooperate in human hematopoietic stem and progenitor cells (HSPCs) during disease progression is still unclear. Here, we integrated clinical and molecular profiling of patients with SF3B1 mutations with gene editing of primary and iPSC-derived human HSPCs to show that high-risk co-mutations impart distinct effects on lineage programs of SF3B1-mutant HSPCs. Secondary RUNX1 or STAG2 mutations were clinically associated with advanced disease and reduced survival. However, RUNX1 and STAG2 mutations induced opposing regulation of myeloid transcriptional programs and differentiation in SF3B1-mutant HSPCs. Moreover, high-risk RUNX1 and STAG2, but not low-risk TET2, mutations expanded distinct SF3B1-mutant HSPC subpopulations. These findings provide evidence that progression from low- to high-risk MDS involves distinct molecular and cellular routes depending on co-mutation patterns.

overall_design:
RNA-seq was performed on FACS-sorted gene edited 5F-HPCs with SF3B1 mutation or wild-type SF3B1, and clonally derived K562 cells. For SF3B1 mutant or wild-type 5F-HPCs, gene expression of RUNX1 or STAG2 edited cells was compared to AAVS1 gene edited controls. For clonally derived K562 cells, splicing profiles of SF3B1 mutant lines with AAVS1, RUNX1 or STAG2 editing was compared to SF3B1 wild-type control edited cells. Raw and processed data for SF3B1 wild-type and single-mutant cells were previously deposited under accession number GSE263299 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE263299).

***************************************************************
The table below lists GEO accessions reused/reanalyzed for this study.
***************************************************************

first: Courtnee

last: Clough

first: Anna

last: Gallì

first: Cristina

last: Picone

first: Beatrice

last: Ferrari

first: Edie

middle: I

last: Crosse

first: Nelli

last: Aydinyan

first: Philip

last: Creamer

first: Sara

last: Pozzi

first: Elisabetta

last: Molteni

first: Chiara

last: Elena

first: Robert

middle: K

last: Bradley

first: Luca

last: Malcovati

first: Sergei

last: Doulatov


title: Molecular basis of positional memory in limb regeneration [RNA-seq]

city: Vienna

first: Elly

last: Tanaka

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP (Research Institute of Molecular Pathology)

summary: Amputation of a salamander limb triggers anterior and posterior connective tissue cells to form distinct signalling centres that together fuel regeneration. Anterior and posterior identities are established during development and are thought to persist lifelong in the form of positional memory. However, neither the molecular basis of positional memory nor whether positional memory can be altered is known. Here, we identify a positive feedback loop responsible for posterior identity in the axolotl (Ambystoma mexicanum) limb. Posterior cells express residual Hand2 transcription factor from development, which primes them to form a Shh signalling centre after limb amputation. During regeneration, Shh signalling is also upstream of Hand2 expression. After regeneration, Shh is shut down but Hand2 is sustained, safeguarding posterior memory. We exploited this regeneration circuitry to convert anterior cells to a posterior cell memory state. Transient exposure of anterior cells to Shh during regeneration kick-started an ectopic Hand2-Shh loop, leading to stable Hand2 expression and a lasting competence to express Shh. Our results implicate positive feedback in the stability of positional memory and reveal that positional memory is more easily reprogrammed in one direction (anterior to posterior) than the other. Modifying positional memory in regenerative cells changes their signalling outputs, which has implications for tissue engineering.

overall_design: We wanted to identify anterior-posterior identity transitions induced in axolotl cells after transplantation or after misexpression of Hand2. This GEO accession includes RNA sequencing data from 6 sample types. We sequenced FACS purified anterior and posterior blastema cells from regenerating axolotl limbs and prepared libraries with higher RNA input (45 ng per sample, 4 replicates each) or lower RNA input (4.5 ng, 4 replicates each). We also sequenced anterior cells transplanted to the anterior or posterior of a host axolotl limb to see what gene expression changes occur (4.5 ng input, 2 replicates each). We also sequenced anterior blastema cells misexpressing exogenous mCherry-Hand2 or, as a control, mCherry only (0.7 ng input, 3 and 2 replicates respectively).

first: Leo

last: Otsuki


title: Aging promotes reactivation of the Barr body at distal chromosome regions [ATAC]

city: Munich

first: Sarah

last: Hoelzl

state: Bavaria

address: Biedersteiner Str. 29

department: Institute of Pharmacology and Toxicology

country: Germany

institute: Technical University of Munich

summary: Decades ago, evidence of age-related reactivation of a single gene on the female inactive X chromosome was observed in mice. While stable silencing of the Barr body is crucial for balancing gene dosage between sexes, it remained unclear whether silencing is maintained during aging. Here, we employed allele-specific multi-omics approaches to capture a comprehensive catalog of genes escaping X chromosome inactivation throughout mouse development and aging. We found substantially elevated escape rates during aging across organs, occurring in multiple distinct cell types and concentrated at distal chromosome regions. Consistently, chromatin accessibility was increased across multiple megabases at chromosome ends, affecting regulatory elements of escapees. Since several age-specific escapees are linked to human diseases, their elevated expression in females might contribute to sex-biased disease progression observed during aging.

overall_design: ATAC-seq from adult (9w) and aged (78w) kidney and liver of C57BL/6J∆XistxCAST/EiJ female mice

first: Daniel

last: Andergassen


title: Aging promotes reactivation of the Barr body at distal chromosome regions [snRNA]

overall_design: single-nucleus RNA-seq from adult (9w) and aged (78w) heart of C57BL/6JxCAST/EiJ female mice


title: Aging promotes reactivation of the Barr body at distal chromosome regions [RNA Major cardiac cell types]

overall_design: RNA-seq from major cardiac cell types (cardiac fibroblasts, cardiomyocytes, endothelial cells, and macrophages) of 9-week-old C57BL/6J∆XistxCAST/EiJ mice


title: RNA polymerase II elongation study along yeast cell cycle.

city: Burjassot

first: Jose

middle: E.

last: Perez-Ortin

state: Valencia

address: Dr. Moliner 50

department: Bioquimica y Biologia Molecular

country: Spain

institute: Universitat de Valencia

summary: Increasing evidence supports that the activity of RNA polymerase II (RNA pol II) during transcription elongation can be regulated to control transcription rates. Using genomic run-on (GRO) and RNA pol II chromatin immunoprecipitation (RPCC), we have respectively measured active and total RNA pol II present in the body of genes at 3 different stages of the mitotic cell cycle of Saccharomyces cerevisiae: G1, S and G2/M. Comparison of active and total RNA pol II values at these three points defined several gene clusters that reflect different patterns of transcription elongation control across the cell cycle. Previously defined cycling genes were overrepresented in some of these clusters, which showed cyclic average mRNA expression patterns. One of the clusters with most divergent GRO and RPCC patterns was significantly enriched in genes functionally related to ribosome biogenesis (RiBi). We confirmed that RiBi mRNA expression upregulates after START. Finally, we analysed the contribution of mRNA stability to each cluster and found that concerted control of RNA pol II activity and mRNA decay is needed to fully understand alternative strategies of gene expression across the cell cycle.

overall_design: After alpfa-factor synchronization cells were taken for GRO and RPCC analysis at three times: 0 (start), 30 min and 60 min after alpha-factor release. GRO samples were normalized by genomic DNA hybridization of the same macroarray (Filter F1-F7). For RPCC analysis cells were used for chromatin immunoprecitation of RNA pol II using an specific antobody. RPCC samples were obtained by normalization of the IP samples by the WCE samples hybridized in the same macroarray.

first: José

middle: E

last: Pérez-Ortín

last: García-Martínez

first: Douglas

last: Maya-Miles


title: Aging promotes reactivation of the Barr body at distal chromosome regions [RNA organs]

overall_design: RNA-seq from embryonic (E14.5), young (4w), adult (9w), and aged (78w) organs of C57BL/6J∆XistxCAST/EiJ mice (brain, heart, kidney, liver, lung, muscle, spleen).


title: Root transcriptional profile of maize seedlings supplied with FePO4 nanoparticles as source of Fe and P.

city: Verona

first: Anita

last: Zamboni

address: Strada Le Grazie, 15

department: Biotechnology

institute: University of Verona

summary: FePO4 nanoparticles (NPs) were used as source of Fe and P for the growth of maize seedlings. Through a series of transcriptional profiles comparison of plants treated with FePO4 NPs, bulk FePO4 (non-nanometric ) and Fe-deficient and P-deficient plants, transcripts speciffically modulated by NPs as source of Fe and P were identified.

overall_design: Twenty-one root samples were analyzed: 3 biological relicates for each of the seven treatement (C, -P, PNP, PB, -Fe, FeNP and FeB).

first: Andrea

last: Ciurli

first: Davide

last: Sega

first: Zeno

last: Varanini


title: Aging promotes reactivation of the Barr body at distal chromosome regions

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

overall_design: Refer to individual Series


overall_design: To identify positional identity genes expressed in the uninjured axolotl limb, we performed gene expression profiling of anterior (2 replicates) and posterior (3 replicates) dermal cells purified from steady state axolotl limb skin by FACS.


title: Parkin activation suppresses antigen presentation of macrophages to promote tumour progression

city: Guangzhou

first: Yan

last: Li

state: Guangdong

address: Sun Yat-sen University, No. 74 Zhongshan Second Road, Yuexiu District, Guangzhou City, Guangdong Province, 510080

institute: Sun Yat-sen University

summary: Here, through a series of in vivo murine tumour progression models, we found that Parkin deficiency inhibit the progression of multiple cancers. scRNA-seq analyses were performed on tumour-infiltrating CD45+ cells sorting from MC38 tumours in WT or Park2-/- mice. scRNA-seq and flow cytometry analyses profiled distinct anti-tumour macrophage subsets and effector T cell subsets in the tumor immune microenvironment of Park2-/- mice, which were further validated by adoptive transfer assays. Mechanistically, Parkin deficiency facilitates MHC-I expression on TAMs through an unconventional AMPK-dependent pathway, thereby yielding antigen-specific T-cell activation and persistent tumoricidal effects. In addition, we found that Park2-/- TAMs-related signature was associated with improved prognosis in solid tumour patients. Our findings underscore Parkin as a negative immune regulator confining intercellular crosstalk between macrophages and T cells that underpins tumour immune evasion, reinforcing Parkin as a promising target for optimizing tumour immunotherapy.

first: Jun

last: Chen

first: Xinyu

last: Wang

first: Yiyi


title: Aberrant ERK signaling in astrocytes impairs learning and memory in RASopathy-associated BRAF mutant mouse models [mouse]

first: Seoyeon

last: Kim

summary: Performed transcriptomic analysis of Nestin;BrafKE/+ and Braf+/+ mice to investigate the molecular basis of BRAF K499E-induced learning and memory deficits.

overall_design: 4 Nestin;BrafKE/+ mice were compared to 5 Braf+/+ control mice.

first: Minkyung

last: Kang

first: Yong-Seok

last: Lee

first: Soowhee

first: Joon-Yong

last: An


title: Aberrant engagement of P-selectin drives hematopoietic stem cell aging

first: Daozheng

last: Yang

address: 1300 Morris Park Ave

institute: Albert Einstein College of Medicine

summary: During aging, hematopoietic stem cell (HSC) function progressively declines which can lead to reduced blood cell production and regeneration, impaired lymphoid cell production and ineffective erythropoiesis. In this study, we uncovered that during aging the cell surface presentation of the type-1 transmembrane protein P-selectin (CD62P, encoded by Selp) increases in a large fraction of HSCs. Notably, expression of P-selectin molecularly and functionally dichotomized the aging HSC pool; stem cells presenting with high abundance of P-selectin were hallmarked by aging-associated gene expression programs and reduced repopulation upon regenerative stress. Overexpression of Selp in young HSCs was sufficient to impair long-term reconstitution potential and repress erythropoiesis. Moreover, IL-1β, which is chronically elevated in the aged bone marrow, triggered Selp expression in HSCs. The aged transcriptome, including Selp, was largely restored when aged HSCs were transplanted to young mice. Mechanistically, we uncovered that appropriate stimulation of P-selectin by its primary ligand, P-selectin glycoprotein ligand-1 (PSGL-1), suppressed aging-associated gene expression and reversely, lack of P-selectin signaling led to HSC premature aging. Collectively, our study uncovered a novel functional role of P-selectin engagement in regulating HSC regeneration and driving stem cell aging when perturbed.

overall_design: In our study, we performed bulk-RNA-seq for (4-6 month) Selp-wild type (SelpWT) and Selp-knock out (SelpKO) hematopoietic stem cells (HSCs). HSCs were either freshly collected and dirrectly for RNA-seq or were treated with P-selectin glycoprotein ligand-1 (PSGL-1) for 24 hours and then collected for RNA-seq.


title: Aberrant ERK signaling in astrocytes impairs learning and memory in RASopathy-associated BRAF mutant mouse models [organoid]

summary: Performed transcriptomic analysis of BRAF K499E homozygous and wildtype organoid to investigate the molecular basis of BRAF K499E-induced learning and memory deficits.

overall_design: 3 BRAF K499E homozygous organoid were compared to 3 wildtype organoid.


title: Aberrant ERK signaling in astrocytes impairs learning and memory in RASopathy-associated BRAF mutant mouse models


title: The polyadenylase PAPI is required for virulence plasmid maintenance in pathogenic bacteria

status: Public on Mar 20 2025

city: Santa Cruz

first: Victoria

last: Auerbuch

address: 1156 High Street

institute: University of California Santa Cruz

summary: Many species of pathogenic bacteria harbor critical plasmid-encoded virulence factors, and yet the regulation of plasmid replication is often poorly understood despite playing key role in plasmid-encoded gene expression. Human pathogenic Yersinia, including the plague agent Yersinia. pestis and its close relative Y. pseudotuberculosis, require the type III secretion system (T3SS) virulence factor to subvert host defense mechanisms and colonize host tissues. The Yersinia T3SS is encoded on the IncFII plasmid for Yersinia virulence (pYV). Several layers of gene regulation enables a large increase in expression of Yersinia T3SS genes at mammalian body temperature. Surprisingly, T3SS expression is also controlled at the level of gene dosage. The number of pYV molecules relative to the number of chromosomes per cell, referred to as plasmid copy number, increases with temperature. The ability to increase and maintain elevated pYV plasmid copy number, and therefore T3SS gene dosage, at 37˚C is important for Yersinia virulence. In addition, pYV is highly stable in Yersinia at all temperatures, despite being dispensable for growth outside the host. Yet how Yersinia reinforces elevated plasmid replication and plasmid stability remains unclear. In this study, we show that the chromosomal gene pcnB encoding the polyadenylase PAP I is required for regulation of pYV plasmid copy number (PCN), maintenance of pYV in the bacterial population outside the host, robust T3SS activity, and Yersinia virulence in a mouse infection model. Likewise, pcnB/PAP I is also required for robust expression of the Shigella flexneri virulence plasmid-encoded T3SS that, similar to Yersinia, is encoded on a virulence plasmid whose replication is regulated by sRNA. Furthermore, Yersinia and Shigella pcnB/PAP I is required for maintaining normal PCN of model antimicrobial resistance (AMR) plasmids whose replication is regulated by sRNA, thereby increasing antibiotic resistance by ten-fold. These data suggest that pcnB/PAP I contributes to the spread and stabilization of sRNA-regulated virulence and AMR plasmids in bacterial pathogens, and is essential in maintaining the gene dosage required to mediate plasmid-encoded traits. Importantly pcnB/PAP I has been bioinformatically identified in many species of bacteria despite being studied in only a few species to date. Our work highlights the potential importance of pcnB/PAP I in antibiotic resistance, and shows for the first time that pcnB/PAP I reinforces PCN andpromotes virulence plasmid stability in natural pathogenic hosts with a direct impact on bacterial virulence.

overall_design: Yersinia pseudotuberculosis IP2666pIB1 strains were grown in 3 mL LB overnight at 26°C and diluted the following morning to an OD600 of 0.2 in 5 mL of fresh LB. Wildtype bacteria in addition to a congenic mutant lacking the pcnB gene as well as a mutant with a transposon insertion upstream of the pYV virulence plasmid cop-rep locus. Each strain was diluted into two separate cultures (one for each temperature). For 26°C samples, cultures were diluted in plain LB media and grown shaking at 26°C for 3 hrs before extracting RNA. For 37°C samples, cultures were diluted into LB low calcium media (containing 20 mM sodium oxalate and 20 mM MgCl2) and grown shaking at 26°C for 1.5 hours before shifting to 37°C to growing shaking for an additional 1.5 hours. After incubating, 1-2 mL of each culture was collected and pelleted for 5 mins at 4,000 rpm (~200 xg).

first: Schubert

last: Katherine

first: Terciano

last: Derfel

first: Auerbuch

last: Victoria


title: Characterizing resistant cellular states in nasopharyngeal carcinoma during EBV lytic induction

city: Hong Kong

first: Xinlei

state: Hong Kong

address: Clear Water Bay, Sai Kung,

department: LIFS

institute: HKUST

summary: The pervasive occurrence of nasopharyngeal carcinoma (NPC) is intricately linked to Epstein-Barr virus (EBV) infection, making EBV and its associated pathways promising therapeutic targets for NPC and other EBV-related cancers. Lytic induction therapy, an emerging virus-targeted therapeutic strategy, capitalizes on the presence of EBV in tumor cells to specifically induce cytotoxicity against EBV-associated malignancies. Despite the expanding repertoire of compounds designed to induce EBV lytic reactivation, achieving universal induction across all infected cells remains elusive. The inherent heterogeneity of tumor cells likely contributes to this variability. In this study, we used a recently generated EBV-positive NPC cell line, named NPC43, as the in vitro model for NPC, and employed single-cell transcriptomics to delineate the diverse responses of NPC43 cells to lytic induction of EBV. Our longitudinal monitoring revealed a distinctive lytic induction non-responsive cellular state characterized by elevated expression of SOX2 and NTRK2. Cells in this state exhibit phenotypic similarities to cancer stem cells (CSCs), and we verified the roles of SOX2 and NTRK2 in manifesting these phenotypes. This discovery underscores a limitation in lytic induction efficacy, suggesting that not all tumor cells are susceptible to this treatment, highlighting the importance of integrating lytic induction with other targeted approaches during therapy.

overall_design:
Untreated NPC43, NPC43 treated with TPA for 8 hours and 24 hours are subject to sinlge cell RNA-sequencing.
Untreated C666-1; C666-1 treated with NaB for 24 hours and 48 hours are subject to single cell RNA-sequencing.

first: Lei

last: Yu

first: Angela

last: Wu


title: Effects of preconception exposure to rotenone on progeny depend on the degree of maternal toxicity

city: Durham

first: Kinsey

middle: C

last: Fisher

state: NC

address: 124 Science Drive

department: Biology

institute: Duke University

summary: Parental exposure to toxicants can affect progeny health, including when those exposures occur prior to conception. However, most published preconception studies have involved exposures that result in loading of pollutants to gametes, or toxic effects to parents which could indirectly affect germ cell or gamete health. Here, we took advantage of the biology of Caenorhabditis elegans to carry out a preconception study in which we minimized the potential for maternal loading of toxicants, and used an exposure paradigm that either did (high concentration) or did not (low concentration) significantly impact the health of the P0 generation. We hypothesized that preconception exposure to mitochondrial toxicants (rotenone, and in some cases antimycin A or pyraclostrobin) during germ cell and gamete development, at levels not causing P0 toxicity, would impact mitochondrial processes in germ cells or gametes prior to conception, and that changes would be observed in offspring. The high rotenone concentration altered P0 growth, mitochondrial respiration, gene expression, induction of the mitochondrial unfolded protein response, and susceptibility to secondary challenge-induced dopaminergic neurodegeneration. However, we observed minor or no P0 effects at the low concentration. The F1 progeny of both low and high concentrations showed few effects, with most occurring in the high-exposure offspring. The only effects observed in the F1 offspring of the low exposure were a 1.7% decrease in egg size (but size later in development was not different from offspring of controls), and a slightly increased sensitivity to dopaminergic neurodegeneration caused by a secondary rotenone exposure. This study is a follow-up of Mello et. al. 2022 (PMID: 35273616; GEO: GSE195584)

overall_design: Worms were exposed to Rotenone .03 or .5 uM or 0.25% DMSO (control) in liquid culture. P0 samples were subsampled from liquid culture at the L4 stage. For F1 samples, P0's were treated with a 48 hr washout period in liquid culture. They were then bleached to synchronize F1 generation, which were cultured in the same conditions as P0 except for no DMSO or rotenone were added.  Detailed description of experimental methods can be found in Mello et. al. 2022 (doi: 10.3389/fimmu.2022.840272). Libraries were made with 500ng total RNA/sample and 9 PCR cycles.

first: Christina

last: Bergemann

first: Daielle

middle: F

last: Mello

first: Rojin

last: Chitrakar

first: Shefali

last: Bijwadia

first: Javier

last: Huayta

first: Ian

middle: T

last: Ryde

first: Rick

last: Presman

first: Zhiqing

last: Huang

first: Amy

middle: H

last: Herring

first: Susan

last: Murphy

first: L.

last: Baugh

first: Joel

last: Meyer


title: Transcriptional Profile of CD8+ Tregs during aging

city: San Antonio

first: Nu

last: Zhang

state: Texas

address: 7703 Floyd Curl, Medical Building/ 5.025V

institute: UT Health Science Center

summary: Aging is a complex biological process that impacts various physiological functions, including the immune system. Our study investigated the impact of aging on CD8+ regulatory T cells (CD8+ Tregs), which showed a pattern of initial increase up to 12 months, then a decline by 24 months in a C57BL/6 mouse model, unlike memory T cells, which consistently increase with age. Functionally, CD8+ Tregs, irrespective of age, did not produce cytokines in response to TCR stimulation, highlighting a stark functional contrast with memory cells. However, upon IL-15 stimulation, CD8+ Tregs, unlike their memory cell counterparts, demonstrated enhanced cytokine production. Transcriptomic analysis revealed an abundance of Klrk1 (killer cell lectin-like receptor subfamily K member 1) gene transcripts in aging CD8+Tregs. Klrk1 gene encodes Natural Killer Group 2 Member D (NKG2D), an activating receptor NK cells express. This upregulation was specific to CD8+CD122hiLy49+ and absent in CD8+CD122hiLy49-. To explore this correlation further, we utilized a Klrk1-/- mouse and observed an increased CD8+Treg population, suggesting a potential negative regulatory role of NKG2D in CD8+Treg homeostasis. These findings provide critical insights into the aging immune system and underscore the importance of CD8+ Tregs in immune regulation and aging.

overall_design: To identify the transcriptomic changes of CD8+ Tregs during aging, we performed RNA sequncing with FACS sorted CD8+CD44+Ly49+CD122+ Tregs from the splenocytes of mice of young (2-3 month) and old (10-12 month).

first: Saranya

last: Srinivasan

first: Ma

last: Chaoyu