title: Glioblastoma tumorspheres treated with perphenazine (PER) and temozolomide (TMZ)

city: Seoul

first: Kibyeong

last: Kim

address: 50-1, Yonsei-ro, Seodaemun-gu

country: South Korea

institute: Yonsei University

summary: Glioblastoma (GBM), a primary malignant brain tumor, has a poor prognosis, even with standard treatments such as radiotherapy and chemotherapy. In this study, we explored the anticancer effects of the synergistic combination of perphenazine (PER), a dopamine receptor D2/3 (DRD2/3) antagonist, and temozolomide (TMZ), a standard treatment for GBM, in patient-derived human GBM tumorspheres (TSs).

overall_design: GBM TSs were treated with PER, TMZ, and combined of both, then their respective gene expression was measured by RNA sequencing.

first: Jun

middle: P

last: Hong

first: Ran

last: Choi

first: Jin-Kyoung

last: Shim

first: Seok-Gu

last: Kang


title: Wheat earthworm-plant-microbiota interactions

status: Public on Mar 03 2025

city: Heslington, York

first: Sara

last: Franco Ortega

address: Wentworth Way

department: Department of Biology

country: United Kingdom

institute: Centre for Novel Agricultural Products, University of York

type: Expression profiling by high throughput sequencing

summary: Earthworms enhance plant growth but the precise mechanism by which this occurs is not known. An understanding of the mechanism could potentially support changes in agricultural management reducing fertiliser usage and therefore costs and the carbon footprint of agriculture. We conducted a factorial experiment in which 5 strains of wheat were grown in the presence and absence of earthworms under regular watering and droughted conditions. The different wheat strains all responded in a similar fashion. Plant biomass was greater in the presence of earthworms and under regular watering. The presence of earthworms reduced the impact of drought on plant biomass and also slowed down the rate of drying of the droughted soils. Plant nutrient content (N, P, Si) showed no consistent pattern with treatments but total N, P and Si mirrored plant biomass and decreased in the order earthworm-present watered > earthworm-present droughted > earthworm-absent watered > earthworm-absent droughted. Nutrient availability in the soil, as assessed by chemical extractions showed no consistent pattern with treatments. Differential gene expression of plants was greater between watering treatments than between earthworm treatments. Genes that were differentially expressed between the earthworm treatments predominantly related to plant defences, abiotic stress and control of plant growth though a couple were linked to both nitrogen cycling and stress responses. The soil microbiome of the earthworm-present treatments was more associated with nutrient-rich environments, the promotion of plant growth and the suppression of plant pathogens. Our data suggest that enhanced plant growth was due to changes in the microbiome due to earthworm processing of the soil rather than changes in nutrient availability due to the presence of earthworms.

overall_design: Five wheat accession (Accession identifiers 1190336=YoGI_178, 1190451=YoGI_203, 1190779=YoGI_287) from the AE Watkins collection and Shamrock (YoGI_349) from the Gediflux collection (both supplied by the John Innes Centre), and commercially available Skyfall (RAGT) were used to examine the role that the presence/absence of the endogeic earthworm Allolobophora chlorotica have under regular watering or drought conditions. Two plants per accession were grown in soil collected from BSSE field, Leeds experimental farm, following a factorial experiment. The soil used for the experiment was a silt loam with pH of 7.69 ± 0.01 and organic matter content of 3.20 ± 0.06% and it was hand sorted to remove earthworms, large stones and roots. The experiment was carried out in a glasshouse at 20°C±5°C daytime and 16°C±5°C night-time. Plants were germinated on wet tissue paper for 6 days before moving them to the soil. Two seedlings were used for each pot. The plants were watered for the first 38 days and after this time point, the drought pots were no longer watered. Samples were collected on day 53 from the beginning of the experiment. Earthworms were collected from Warren paddock, a pasture field at Leeds experimental farm and three were added to each pot.

first: M

middle: E

last: Hodson

first: P

last: Brailey-Jones

first: W

last: Burns

first: A

middle: L

last: Harper

first: S

last: Hartley

first: T

last: Helgason

first: H

middle: F

last: Walker


title: A prospective, international, multisite comparison of platelet isolation techniques for genome-wide transcriptomics: Communication from the SSC of the ISTH

status: Public on Mar 01 2025

city: Salt Lake City

first: Matthew

middle: T

last: Rondina

state: Utah

department: Hematology

country: USA

institute: University of Utah

summary: Genome-wide platelet transcriptomics is increasingly being used to uncover new aspects of platelet biology and as a diagnostic and prognostic tool. Nevertheless, platelet isolation methods for transcriptomic studies are not standardized, introducing challenges for cross-study comparisons, data integration, and replication. In this prospective multicenter study, we assessed how three of the most commonly-used platelet isolation protocols influence metrics from next-generation bulk RNA sequencing and functional assays. Compared with washing alone, more stringent removal of leukocytes by anti-CD45+ beads or PALL filters resulted in sufficient quantity of RNA for next-generation sequencing and similar quality of RNA sequencing metrics. The more stringent removal of leukocytes resulted in lower relative expression of known leukocyte-specific genes and higher relative expression of known platelet-specific genes. The results were consistent across enrolling sites, suggesting that the techniques are transferrable and reproducible. The use of anti-CD45+ beads reduced integrin aIIbb3 activation to PAR-1 activating peptide (SFLLRN-TRAP) but not ADP, compared to washing alone, while the isolation method had no influence on basal platelet reactivity. In conclusion, genome-wide transcriptional and functional assays in platelets are influenced by isolation technique. These results should help the research community make informed choices about platelet isolation techniques in their own platelet studies.

overall_design: To investigate the effects of platelet isolation on the quality of genome-wide transcriptomics, blood was collected from healthy donors across 4 international sites (University of Utah; Camera, Milan site, Italy; University of Debrecen, Hungary; Perugia, Italy) and split into three modes of isolation, washed platelets, leuckocyte-bead depletion (LDPs), or through PALL-filtration, to isolate platelets. RNA was extracted from isolated platelets. Then, gene expression analysis using data obtained from RNA-seq of platelets from 3 different isolation techniques across 4 sites was performed.

first: Meenakshi

last: Banerjee

first: Jesse

middle: W

last: Rowley

first: Chris

middle: J

last: Stubben

first: Neal

middle: D

last: Tolley

first: Kathleen

last: Freson

first: Benjamin

last: Nelson

first: Bela

last: Nagy Jr

first: Zsolt

last: Fejes

first: Antoinette

middle: M

last: Blair

first: Ernest

last: Turro

first: Paolo

last: Gresele

first: Giulia

last: Ciarrocca Taranta

first: Loredana

last: Bury

first: Emanuela

last: Falcinelli

first: Marie

last: Lordkipanidze

first: Alessi

last: Marie-Christine

first: Andrew

last: Johnson

first: Tamam

last: Bakchoul

first: Sofia

last: Ramstrom

first: Mattia

last: Frontini

first: Marina

last: Camera

first: Marta

last: Brambilla

first: Robert

middle: A

last: Campbell


title: H2A.Z reinforces maternal H3K4me3 formation and is essential for meiotic progression in mouse oocytes [RNA-Seq]

city: Yokohama

first: Azusa

last: Inoue

state: Kanagawa

address: Suehiro-cho 1-7-22, Tsurumi-ku

department: Center for Integrative Medical Sciences

country: Japan

institute: RIKEN

summary: Mammalian oocytes establish a unique landscape of histone modifications, some of which are inherited by early embryos. How histone variants shape the maternal histone landscape remains unknown. Here, we map histone H2A variants in mouse fully grown oocytes (FGOs) and find that H2A.Z forms broad domains across intergenic regions, along non-canonical H3K4me3 (ncH3K4me3). During oocyte growth, H2A.Z progressively transitions from an active promoter-rich, canonical distribution to a non-canonical broad distribution (ncH2A.Z). Depletion of H2A.Z in oocytes partially impairs ncH3K4me3 formation and causes severe defects in meiotic progression, which resemble Mll2-knockout oocytes. Conversely, depletion of ncH3K4me3 by Mll2 knockout also causes a reduction of ncH2A.Z in FGOs. Thus, our study suggests that ncH2A.Z and ncH3K4me3 reinforce each other to form functional oocytes.

overall_design: RNA-seq were performed in H2A.Z control and H2A.Z DKO FGOs, in Mll2 WT and Mll2 KO FGOs. Then comparative analysis was done between these two mutants.

first: Hailiang

last: Mei

first: Ryoya

last: Hayashi

first: Chisayo

last: Kozuka

first: Mami

last: Kumon

first: Haruhiko

last: Koseki


title: YTHDF2 Suppresses the 2C-like State in Mouse Embryonic Stem Cells

city: Nanjing

first: Xiang

last: Wu

address: 639 longmiandadao

country: China

institute: China Pharmaceutical University

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

overall_design: Refer to individual Series


title: HERV activation segregates ME/CFS from fibromyalgia while defining a novel nosologic entity

first: Elisa

middle: Elisa

last: Oltra

state: VALÈNCIA

address: C/ Quevedo 2

department: Pathology

country: Spain

institute: Universidad Catolica de Valencia San Vicente Martir

summary: Research of Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) and Fibromyalgia (FM), two acquired chronic illnesses affecting mainly females, has failed to ascertain their frequent co-appearance and etiology. Despite prior detection of human endogenous retrovirus (HERV) activation in these diseases, the potential biomarker value of HERV expression profiles for their diagnosis, and the relationship of HERV expression profiles with patient immune systems and symptoms had remained unexplored. By using HERV-V3 high-density microarrays (including over 350k HERV elements and more than 1500 immune-related genes) to interrogate the transcriptomes of peripheral blood mononuclear cells from female patients diagnosed with ME/CFS, FM or both, and matched healthy controls (n=43), this study fills this gap of knowledge. Hierarchical clustering of HERV expression profiles strikingly allowed perfect participant assignment into four distinct groups: ME/CFS, FM, co-diagnosed, or healthy, pointing at a potent biomarker value of HERV expression profiles to differentiate between these hard-to-diagnose chronic syndromes. Differentially expressed HERV-immune-gene modules revealed unique profiles for each of the four study groups and highlighting decreased γδ T cells, and increased plasma and resting CD4 memory T cells, correlating with patient symptom severity in ME/CFS. Moreover, activation of HERV sequences coincided with enrichment of binding sequences targeted by transcription factors which recruit SETDB1 and TRIM28, two known epigenetic silencers of HERV, in ME/CFS, offering a mechanistic explanation for the findings. Unexpectedly, HERV expression profiles appeared minimally affected in co-diagnosed patients denoting a new nosological entity with low epigenetic impact, a seemingly relevant aspect for the diagnosis and treatment of this prevalent group of patients.

overall_design: Microarray-based transcriptome evaluation of PBMCs from female patients diagnosed with ME/CFS, FM or both, and matched healthy controls

first: K

last: Giménez-Orenga

first: E

last: Martín-Martínez

first: L

last: Nathanson


title: Ythdf2 Suppresses the 2C-like State in Mouse Embryonic Stem Cells via Cooperation with Cnot1 [RNA-seq]

summary: Mouse embryonic stem cells (ESCs) consist of a rare population of heterogeneous cells which express 2-cell-stage-specific transcripts and are referred to as 2-cell-like cells (2CLCs). Accumulating evidence has demonstrated that transcription factors and epigenetic modifications exert crucial functions in the transition of ESCs to 2CLCs. However, the roles of RNA modification in the regulation of 2C-like state remain elusive. Using Dux-induced 2CLCs system, we examine N6-methyladenosine (m6A) modification landscape in transcriptome-wide, and find that m6A is dynamically regulated during Dux-driven 2C-like reprogramming. Intriguingly, many of 2C-specific transcripts are highly methylated, including Dux and Zscan4 cluster genes. We further identify the m6A reader protein Ythdf2 as a critical regulator of 2C-like state. Depletion of Ythdf2 facilitates robust expressions of 2C transcripts and the transition of ESCs to 2CLCs. Mechanically, Ythdf2 binds to the Dux/Zscan4 transcripts and promotes their degradation through recruiting the key component of RNA deadenylase complex, Cnot1. Consistent with the phenotype of Ythdf2 deficiency, silencing of Cnot1 induces the 2C gene expressions and the transition of ESCs into the 2C-like state. Collectively, our findings reveal novel insights into the epitranscriptomic regulation of the 2C-like state in mouse ESCs.

overall_design: RNA sequencing in mouse embryonic stem cells (mESCs) treated with shYthdf2 or shScramble

first: Junjie

last: He

first: Wanting

last: Cai


title: H2A.Z reinforces maternal H3K4me3 formation and is essential for meiotic progression in mouse oocytes

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: CATCH-seq and CUT&RUN of canonical H2A and H2A variants, including H2A.Z and TH2A, in fully grown oocytes. CATCH-seq of H2A.Z in oocytes from 4 stages, including primary (5 days), secondary (10 days), preantral (15 days) stage of growing oocytes, and the fully grown stage of oocyte (28 days FGO) were conducted to profiling H2A.Z's landscape. Also, CATCH-seq of 10d growing oocytes with control and amanitin treated were performed. H2A.Z, H3K4me3, H3K27me3 and H2AK119ub1 CATCH-seq were performed in H2A.Z control and H2A.Z DKO FGO oocytes. H2A.Z and H3K4me3 CATCH-seq were performed in Mll2 wild type and Mll2 KO FGO oocytes.


title: Transcriptome mapping of bone fracture identifies Notch signaling as an important regulator of skeletal repair

city: Farmington

first: Sanja

last: Novak

state: CT

address: 263 Farmington Ave

institute: UConn Health

summary: We present a transcriptomic analysis that provides a better understanding of regulatory mechanisms within the healthy and injured periosteum leading to novel translational approaches for bone healing. The focus of this work is on the early regulatory control of bone healing by completing a transcriptomic analysis of forming periosteal callus cells on day 3 post fracture. Based on our previous work indicating that induced Notch1 signaling in osteoprogenitors leads to better healing, we contrasted samples in which Notch 1 intracellular domain (NICD1) is overexpressed by periosteal stem/progenitor cells with control unperturbed periosteum. We determined molecular mechanisms and changes in skeletal stem/progenitor cells (SSPC) and other cell populations within callus including hematopoietic lineages. Notch ligands were differentially expressed in endothelial and mesenchymal populations, with Dll4 restricted to endothelial cells while Jag1 expressed by various mesenchymal populations. When targeting deletion of Dll4 in SSPCs using a-smooth muscle actin (aSMACreER) in mesenchymal cells there was no phenotype, while deletion in EC using Cdh5CreER exhibited negative effects on the early fracture healing. Translation of these observations into clinically relevant model of bone healing revealed the positive effects of combination of Notch ligands delivery with currently used osteogenic inducer BMP2.

overall_design: Single cell RNA sequencing (sc RNA-seq) was performed from intact and fractured periosteal cells (3 days after the fracture) in aSMACre+/NICD1 and Cre-/NICD1 mice. To induce NICD1 overexpression Cre- and Cre+ mice were injected with tamoxifen (75 mg/kg) on a day of fracture and 2 dpf (or if intact, 3 and 1 day before sacrificing animals). Three animals of each group were sacrificed and periosteum (intact) or periosteal callus (fractured) were pooled and digested as previously described (13, 42) using Collagenase P (Roche, IN, USA), hyaluronidase (Sigma Aldrich, St Louis, MO, USA) digestion for 1 h on 37°C with shaking. Live, mesenchymal (CD45-) and hematopoietic (CD45+) cells were sorted and single cell RNA-seq performed (10x Genomics). Periosteal cells were digested, stained for CD45-eFluor 450, Ter119-APC and propidium iodide to exclude dead cells. CD45-Ter119- and CD45+Ter119+ were sorted (BD FACSSymphonyTM S6 Cell Sorter) and twelve thousand live cells were loaded into 10X Chromium X controller with ~10,000 cells cell barcoded for RNA-seq using a Chromium Single Cell 3' Reagent Kits v3.1. Libraries were sequenced on a NovaSeq 6000 S4 flow cell lane (Illumina) with an average sequencing depth of 100,000 reads per cell for CD45- and 50,000 reads per cell for CD45+. For FASTQ generation and alignments, Illumina basecall files were converted to FASTQs using bcl2fastq v2.20.0.422 (Illumina) and FASTQ files associated with the gene expression libraries aligned to the mm10 genome using the version 3.1.0 Cell Ranger count pipeline (10x Genomics).

first: Hitoshi

last: Tanigawa

first: Vijender

last: Singh

first: Sierra

middle: H

last: Root

first: Tannin

last: Schmidt

first: Kurt

last: Hankenson

first: Ivo

last: Kalajzic


title: Ythdf2 Suppresses the 2C-like State in Mouse Embryonic Stem Cells via Cooperation with Cnot1 [RIP-seq]

overall_design: RIP-seq in mouse embryonic stem cells (mESCs) following 24-hour treatment with Dox using anti-Ythdf2 antibody

first: Xiao-Min

last: Liu


title: RNA seq for NS2A and empty vector overexpressed HEK239T cells

city: Jiangsu suzhou

first: Jingfei

last: Zhu

state: CN

address: Chongwen Road 215123

institute: ISM

summary: Study the effect of NS2A on the transcriptome of mammalian cells upon overexpression

overall_design: Transfecting NS2A or empty vector into HEK293T cells for 24 hours and extracting total RNA for sequencing


title: RNA seq for BMDMs from WT and NS2AmKI mice

overall_design: Harvesting BMDMs from WT and NS2AmKI mice and extracting total RNA for sequencing


title: Psychedelic control of neuroimmune interactions governing fear

status: Public on Mar 02 2025

city: Boston

first: Michael

last: Wheeler

state: MA

address: 60 Fenwood Rd.

department: Neurology

institute: Brigham and Women's Hospital

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

first: Elizabeth

middle: N

last: Chung

first: Jinsu

last: Lee


title: Continuous expression of TOX safeguards exhausted CD8 T cell epigenetic fate [coassay_TOXKO]

city: Philadelphia

middle: JOHN

last: WHERRY

state: PA

address: 421 Curie Blvd,354 BRB II/III

department: Systems Pharmacology       and Translational Therapeutics,Institute for Immunology

institute: University of Pennsylvania

summary: CD8 T cell exhaustion is a major barrier limiting anti-tumor therapy. Though checkpoint blockade temporarily improves exhausted CD8 T cell (Tex) function, the underlying epigenetic landscape of Tex remains largely unchanged, preventing their durable “reinvigoration.” Whereas the HMG-box transcription factor TOX has been identified as a critical initiator of Tex epigenetic programming, it remains unclear whether TOX plays an ongoing role in preserving Tex biology after cells commit to exhaustion. Here, we decoupled the role of TOX in the initiation versus maintenance of CD8 T cell exhaustion by temporally deleting TOX in established Tex cells. Induced TOX ablation in committed Tex resulted in apoptotic-driven loss of Tex, reduced expression of inhibitory receptors including PD-1, and a pronounced decrease in terminally differentiated subsets of Tex cells. Simultaneous gene expression and epigenetic profiling revealed a critical role for TOX in ensuring ongoing chromatin accessibility and transcriptional patterns for key Tex gene modules in committed Tex cells. Moreover, when exposed to strong effector-differentiation signals, established Tex in which TOX had been deleted acquired an altered chromatin landscape with increased accessibility at cytotoxic genes typically accessible in Teff cells, undergoing partial reprogramming into a more functional state. Together, these findings suggest that continuous TOX expression in established Tex functions as a durable epigenetic barrier to reinforce the Tex developmental fate by simultaneously maintaining Tex epigenetic commitment while restraining effector reprogramming. Manipulation of TOX even after Tex establishment could therefore provide a therapeutic opportunity to rewire Tex biology in settings of chronic infection or cancer

overall_design: Cells from inducible-Cre (Rosa26CreERT2/+Toxfl/fl P14) mice where TOX was temporally deleted from mature populations of LCMV-specific T exhausted cells after establishment of chronic LCMV infection 5 days post infection were subjected to scRNA and scATACseq coassay,naive cells and WT cells were used as controls

first: Yinghui

last: Huang

last: Wherry


title: Single-nucleus RNA sequencing of human fetal leptomeninges

city: Shanghai

first: Qi

last: Dashi

address: 450 Tengyue Road

department: Center for Clinical Research and Translational Medicine, Yangpu Hospital

institute: Tongji University, Shanghai

summary: To investigate the development of human leptomeninges and their co-development with the brain. Nuclei were extracted from eight human fetal leptomeninges obtained from aborted embryos, ranging from PCW8 to PCW21 (post-conceptional weeks). The entire arachnoid mater, pia mater, associated blood vessels, and immune cells were included for single-nucleus RNA sequencing (snRNA-seq).

overall_design: The leptomeninges intended for single-nucleus RNA sequencing were meticulously dissected from the forebrain of the cerebrum. The samples included the entire arachnoid mater, pia mater, associated blood vessels, and resident immune cells. After careful peeling, the leptomeninges were immersed in ice-cold collection buffer, washed with PBS, and then subjected to nuclear isolation.

first: Dashi

last: Qi


title: METTL3 dictates the development of thymocytes via restraining ferroptosis program during age related thymic involution

city: wuhan

first: huiru

last: jing

address: Donghu Road, No. 115, Wuchang District, Wuhan, Hubei Province

institute: wuhan university

summary: Thymic involution is a crucial factor in immune system aging and results in age-related impairment of T cell responses. The control of programmed cell death plays a fundamental role in thymocytes development. How thymocytes cell death contribute to thymic involution remains elusive. In this study, we found that METTL3 is highly expressed in double positive (DP) cells from young mice but decreased in aged mice. Mice conditionally deficiency for METTL3 in T cells showed thymic involution phenotypes with decreased survival and increased senescent DP cells. Additionally, METTL3 deficiency elicited ferroptosis program rather than other cell death pathways and led to defective DP cell development. Furthermore, GPX4, a molecule that protects cells from ferroptosis, was essential for thymocyte survival and preventing senescence. Mechanistically, GPX4 was maintained by METTL3 at the translation level in METTL3 methyltransferase activity independent manner. Targeting METTL3 and ferroptosis process promoted DP cell survival and reinvigorated aged DP cells. These findings reveal the central role of the METTL3-GPX4-ferroptosis axis in regulating thymocyte homeostasis and identifying targets for impeding age-related thymic involution and diseases.

overall_design: The thymic DP cells from young WT, young METTL3 KO, old WT and METTL3 KO mice were obtained through flow cytometry sorting.


title: Effect of interleukin-1beta on confluent human lymphatic endothelial cells

status: Public on Feb 28 2025

city: Rouen

first: Ebba

last: Brakenhielm

address: Inserm U1096

country: France

institute: Inserm

summary: The goal of the study was to examine the transcriptional changes in human lymphatic endothelial cells (LEC) stimulated by interleukin-1beta

overall_design:
RNAseq profiling of human LECs (HMVEC-dLy) cultured until confluent and then serum-starved (1% FCS) overnight, followed by exposure  during 24h to 20 ng/mL human recombinant IL1beta. Controls were treated the same way without addition of IL1beta. N=3 samples per group.

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first: Coraline

last: Heron

first: Theo

last: Lemarcis

first: Oceane

last: Laguerre

first: Benjamin

last: Bourgeois

first: Corentin

last: Thuilliez

first: Chloe

last: Valentin

first: Anais

last: Dumesnil

first: Manon

last: Valet

first: David

last: Godefroy

first: Damien

last: Schapman

first: Gaetan

last: Riou

first: Sophie

last: Candon

first: Celine

last: Derambure

first: Caroline

last: Berard

first: Helene

last: Dauchel

first: Virginie

last: Tardif


title: STimulator of INterferon Genes (STING) primed intra-articular cellular therapy improves gait and histologic outcomes in a murine osteoarthritis model

city: Fort Collins

first: Steven

last: Dow

state: CO

address: 300 W Drake Rd

department: Clinical Sciences

institute: Colorado State University

summary: We report here the histological, transcriptomic, and movement characteristics for mice who received nonactivated and activated MSC cellular therapy, post-operatively, in a surgically induced destabilization of the medial meniscus. Treatment with STING & TLR3 activated MSCs significantly improved histological, transcriptomic, and movement parameters in the mice – with TLR3-MSCs not achieving significant improvement in the movement parameters. These findings can provide an approach to cellular therapies for osteoarthritis and potentially a mechanism to adjust the treatment based upon the severity/duration of degeneration. This paper further adds functional information regarding STING-MSC, TLR3-MSC, and nonactivated MSCs cellular therapy and further supports studies and literature regarding their usage in the context of regenerative therapies and alleviation of burdensome osteoarthritic symptoms.

overall_design: Studies were performed using 12-week-old male C57BL/6Nci mice (Charles River Laboratories, Wilmington, MA, USA). Mice (n=10 per group) were randomly assigned to receive surgery followed by either needle insertion alone, non-activated MSC, pIC-activated MSC (TLR3), or STING-activated MSC

first: Lyndah

last: Chow

first: Lynn

last: Pezzanite

first: Kelly

last: Santangelo


title: Essential angiosperm-specific subunits of HDA19 histone deacetylase complexes in Arabidopsis [ChIP-Seq]

city: Beijing

first: xinjian

last: He

address: No. 7, zhongguancun life science park road, changping district

institute: National Institute of Biological Sciences

summary: Although the Arabidopsis thaliana histone deacetylase HDA19 and its close homolog HDA6 form SIN3-type histone deacetylase complexes, they display distinct biological roles, with the reason for these differences being poorly understood. We has identified three angiosperm-specific HDA19-interacting homologous proteins, termed HDIP1, HDIP2, and HDIP3 (HDIP1/2/3). These proteins interact with HDA19 and other conserved histone deacetylase complex components, leading to the formation of HDA19-containing SIN3-type complexes, while they are not involved in the formation of HDA6-containing ones. While mutants of conserved SIN3-type complex components show phenotypes divergent from the hda19 mutant, the hdip1/2/3 mutant closely mirrors the hda19 mutant in development, abscisic acid signaling, and drought stress tolerance. Omics analyses indicate that HDIP1/2/3 and HDA19 co-occupy chromatin and jointly repress gene transcription, especially for stress-related genes. An α-helix motif within HDIP1 has the capacity to bind to nucleosomes and architectural DNA, and is required for its function in Arabidopsis plants. These findings suggest that the angiosperm SIN3-type complexes have evolved to include additional subunits for the precise regulation of histone deacetylation and gene transcription.

overall_design: Examination of protein binding levels in transgenic plants;

first: XinJian


title: Essential angiosperm-specific subunits of HDA19 histone deacetylase complexes in Arabidopsis

summary: While both the histone deacetylase HDA19 and its close homolog HDA6 can form SIN3-type histone deacetylase complexes, they display specialized biological roles, with the mechanisms of their functional specificities largely unclear. In this study, we identified three previously uncharacterized homologs designated as HDA19-interacting proteins 1, 2, and 3 (HDIP1/2/3). These homologs not only interact with HDA19 but also with other components of the SIN3-type histone deacetylase complexes, including SNLs, MSI1, and HDC1, thereby facilitating the assembly of HDA19-containing complexes but not HDA6-containing ones. HDIP1/2/3 orthologs are found in angiosperms but are absent in other plant species. The hdip1/2/3 and hda19 mutants exhibit highly similar phenotypes in terms of development, abscisic acid response, and drought tolerance. Omics data indicate that HDIP1/2/3 and HDA19 co-occupy chromatin and co-repress gene transcription, particularly at those genes associated with stress responses. An a-helix motif in HDIP1 is capable of binding to the nucleosome as well as the four-way junction DNA that mimics the DNA entry and exit sites of the nucleosome, and is essential for the function of HDIP1 in Arabidopsis plants. These findings suggest that the HDA19-containing SIN3-type histone deacetylase complexes have incorporated additional subunits in angiosperms to support the intricate regulation of histone deacetylation and gene transcription during plant development and stress responses.

overall_design: Examination of the mRNA expression of 20-day-old wild type and two mutants in Arabidopsis

first: Xin-Jian


title: Harnessing the evolved bacteria as cystine-addicted living biocatalyst for antitumor metabolic therapy

city: Wuhan

first: Yu-Zhang

last: Wang

address: Mt Luojia

institute: Wuhan University

summary: Bacteria-based metabolic therapy has been acknowledged as a promising strategy for tumor treatment. However, the insufficient efficiency of wild-type bacteria severely restricts their therapeutic efficacy. Here, we successfully develop a ʟ-cystine (CySS)-addicted bacterial biocatalyst for metabolic therapy through a dual-selection directed evolution strategy. Our evolved strain (namely SFEc+) exhibits a 36-fold increase in CySS uptake and a 23-fold improvement in total activity of cysteine desulfhydrases compared to the wild-type strain. By conjugating with DMXAA-loaded liposomes, the engineered biocatalyst not only prevents the influx of nutrients into the tumor microenvironment by blocking neovasculature but also achieves efficient and durable CySS catabolism locally. The absence of CySS disrupts redox homeostasis in tumor cells and strikingly increases intracellular ROS level, resulting in effective tumor elimination. In multiple murine tumor models, intravenous administration of the engineered living biocatalyst displays favorable therapeutic outcomes. Our work not only highlights the promise of directed evolution strategy in enhancing the stability and efficiency of bacteria-based living biocatalyst, but also provides the new opportunities in antitumor metabolic therapy.

overall_design: To underlie the mechanisms of the global reprogramming of SFEc+'s metabolic network , we performed a comprehensive transcriptomic analysis to compare the genetic expression profiles between SFEc+ and Ec.

first: Wei-Hai

last: Chen

first: Zi-Yi

last: Han

first: Shi-Man

last: Zhang

first: Ping

last: Ji

first: Jun-Long

last: Liang

first: Xian-Zheng


title: SARS-CoV2 infection triggers reactive astrocyte states and inflammatory conditions in Human Cortical Organoids

city: Liege

first: Ira

middle: Mercedes

last: ESPUNY CAMACHO

state: Liege

address: Avenue de l'Hôpital,11

department: Département des sciences biomédicales et précliniques

country: Belgium

institute: Uliege

summary: SARS-CoV2, severe acute respiratory syndrome coronavirus 2, is frequently associated with neurological manifestations. Despite the presence of mild to severe CNS-related symptoms in a cohort of patients, there is no consensus whether the virus can infect directly brain tissue or if the symptoms in patients are a consequence of peripheral infectivity of the virus. Here, we use a human stem cell-derived cortical organoid model to assess SARS-CoV2 infectivity of brain cells and unravel the cell-type tropism and its downstream pathological effects. Our results show consistent and reproducible low levels of SARS-CoV2 infection in human cortical organoids at different maturation stages in vitro. We found that astrocytes, deep projection neurons, upper callosal neurons and inhibitory neurons were infected by SARS-CoV2. Interestingly, astrocytes showed the highest infection rate among all infected cell populations that led to increased presence of reactive states. Further, transcriptomic analysis revealed overall changes in expression of genes related to oxidative phosphorylation, TNFA signaling, astrocyte activation and metabolic changes. Thus, local and minor infectivity of SARS-CoV2 in the brain may induce widespread adverse effects in brain cell populations.

overall_design: Brain organoids of 6M are analyzed as CTRL or have been exposed to SARS-CoV2 for 3h and collected 72h post infection. We have four biological replicates coming from 2 independent batches for each condition

first: M

last: Colinet

first: I

last: Chiver

first: A

last: Bonafina

first: G

last: Masset

first: D

last: Almansa

first: E

last: Di Valentin

first: J

middle: C

last: Twizere

first: L

last: Nguyen

last: Espuny-Camacho


title: Histone protein-dependent cisplatin resistance in OSCC: in vivo and in vitro spheroid and organoid model

city: Daegu

first: Su Young

last: Oh

address: 2177, Dalgubeol-daero, Jung-gu

institute: Kyungpook National University

summary:
Cisplatin is one of the most potential and widely used drugs for oral cancer chemotherapy. However, although cisplatin resistance occurs frequently, it is difficult to predict the therapeutic efficacy before clinical trial.
We tried to predict cisplatin resistance by comparing the gene expression pattern between cisplatin-sensitive UMSCC1 cells and paired cisplatin-resistant UM-Cis cells.

overall_design: To analyze the difference in gene expression levels between UMSCC1 and UM-Cis cells, microarray analysis was attempted on a total of 6 samples with each cell line in triplicate using the Affymetrix GeneChip® Human Gene 2.0 ST array (Affymetrix Inc., Santa Clara, CA, US) containing 40,716 gene-level probe set.

first: Su-Hyung

last: Hong

first: Su

middle: Y


first: xinjian

last: He

overall_design: Refer to individual Series

first: Xin-Jian


title: A detailed analysis of second and third generation sequencing approaches for accurate length determination of short tandem repeats and homopolymers [TypeII_Illumina]

status: Public on Feb 27 2025

city: Paris

first: Yimin

last: SHEN

state: Val-de-Marne

address: 27 Rue Juliette Dodu

institute: Fondation Jean Dausset-CEPH

summary: Microsatellites are short tandem repeats (STRs) of a motif of 1 to 6 nucleotides that are ubiquitous in almost all genomes and widely used in many biomedical applications. However, despite the development of next-generation sequencing (NGS) over the past two decades with new technologies coming to the market, accurately sequencing and genotyping STRs, particularly homopolymers, are still very challenging today due to several technical limitations. This leads in many cases to erroneous allele calls and difficulty in correctly identifying the genuine allele distribution in a sample. In the present study, we assessed several second and third NGS approaches in their capability to correctly determine the length of microsatellites using plasmids containing A/T homopolymers, AC/TG or AT/TA dinucleotide STRs of variable length. Standard PCR-free and PCR-containing, single Unique Molecular Index (UMI) and dual UMI ‘duplex sequencing’ protocols were evaluated using Illumina short-read sequencing, and two PCR-free protocols using PacBio and nanopore long-read sequencing. Several bioinformatics algorithms were developed to correctly identify microsatellite alleles from sequencing data, including four and two modes for generating standard and combined consensus alleles, respectively. We provided a detailed analysis and comparison of these approaches and made several recommendations for the accurate determination of microsatellite allele length.

overall_design: Microsatellite (A15, A20, A25, (AC)15, (AC)20, (AC)25, (AT)15, (AT)20 and (AT)25 contained in plasmids analyzed with different types of second and third generation sequencing protocols.

first: Sophie

middle: I

last: Jeanjean

last: Shen

first: Lise

last: Hardy

first: Antoine

last: Daunay

first: Marc

last: Delépine

first: Zuzana

last: Gerber

first: Antonio

last: Alberdi

first: Emmanuel

last: Tubacher

first: Jean-François

last: Deleuze

first: Alexandre

last: How-Kit


title: A detailed analysis of second and third generation sequencing approaches for accurate length determination of short tandem repeats and homopolymers [TypeIV_PacBio]


title: Age-associated modulation of TREM1/TREM2 expressing macrophages promotes melanoma progression and metastasis

city: La Jolla

first: Ze'ev

middle: A.

last: Ronai

state: CA

address: 10901 North Torrey Pines Road

department: Tumor Initiation and Maintenance Program, NCI-Designated Cancer Center

institute: Sanford Burnham Prebys Medical Discovery Institute

summary: Aging is a known risk factor for melanoma, yet the mechanisms underlying melanoma progression and metastasis in the older population remain largely unexplored.  Among remaining gaps is the role of changes in melanoma microenvironment in key phenotypes exacerbated by age. Here we demonstrate that age enriches immunosuppressor tumor microenvironment which can be linked with melanoma metastasis phenotype. Age-associated macrophages with a tolerogenic phenotype and dysfunctional CD8 positive cells with an exhausted phenotype were identified in melanomas of aged mice and human. Macrophages of the older population were enriched of the immunosuppressor subcluster expressing Trem2 while the profibrotic subcluster expressing Trem1 was reduced. Notably, inhibition of TREM1 decreased melanoma growth in young but not old mice, whereas inhibition of TREM2 prevented lung metastasis in aged mice. These data identify novel targets in melanoma metastasis which may guide aged-dependent immunotherapies.

overall_design: Single cell gene expression analysis of melanoma Cd45 cells in 4-, 12-, and 20-months old mice using PIP-seq

first: Marzia

last: Scortegagna

first: Ze’ev


title: A detailed analysis of second and third generation sequencing approaches for accurate length determination of short tandem repeats and homopolymers [TypeI_Illumina]


title: Rescuing early Parkinson-induced hyposmia prevents dopaminergic system failure [fruit fly]

city: Basel

first: Jasper

last: Janssens

address: Mattenstrasse 26

department: DBSSE

country: Switzerland

institute: ETH Zurich

summary:
The diagnosis of Parkinsonism is based on motor symptoms that are caused by reduced dopaminergic output
However, decades earlier, patients report non-motoric problems, including hyposmia
It is not known if non-motor and motor defects are causally connected
Here we used single-cell transcriptome sequencing (10x) of young and olf fly mutants (whole brain)
and human patients (three regions: nucleus basalis of Meynert, nucleus accumbens and putamen).
This atlas reveals early defects in cholinergic neurons that are recapitulaed across species

overall_design: scRNA (10x Genomics) of fresh fly brains

first: J

first: U

last: Pech

first: S

last: Aerts

first: P

last: Verstreken


title: ChIPseq in Acly wild-type or conditional KO mouse T-ALLs

status: Public on Feb 25 2025

city: New Brunswick

first: Daniel

last: Herranz

state: New Jersey

address: 195 Little Albany St

institute: Rutgers Cancer Institute of New Jersey

summary: C57BL6 mice harboring Acly conditional knockout NOTCH1-ΔE-induced leukemias were treated with vehicle (control) or tamoxifen to induce isogenic deletion of Acly.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for histone modifications H3K27ac, H3K9acc, and H3K4me3 in mice

first: Amartya

last: Singh

first: Victoria

last: da Silva-Diz


title: Epigenetic control of replication, gene expression and growth phase by ADP-ribosylation of DNA in Mycobacterium tuberculosis [RNAseq_TPEN]

status: Public on Feb 26 2025

city: Guildford

first: Graham

last: Stewart

address: Stag Hill, University Campus, Guildford GU2 7XH

institute: University of Surrey

summary: Mycobacterium tuberculosis maintains long-term infections characterised by the need to regulate growth and adapt to contrasting in vivo environments. Here we show that M. tuberculosis complex bacteria utilise reversible ADP-ribosylation of single-stranded DNA as an epigenetic mechanism to coordinate stationary phase growth with transcriptional adaptation. The DNA-modification is controlled by DarT, an ADP-ribosyl transferase, which adds ADP-ribose to thymidine, and DarG, which enzymatically removes this base modification. Using darG-knockdown M. bovis BCG, we map the first DNA-ADP-ribosylome from any organism. We show that inhibition of replication by DarT is reversible and accompanied by extensive ADP-ribosylation at the origin of replication (OriC). In addition, we observe ADP-ribosylation across the genome and demonstrate that ADP-ribose-thymidine alters the transcriptional activity of M. tuberculosis RNA polymerase. Furthermore, we demonstrate that during stationary phase, DarT-dependent ADP-ribosylation of M. tuberculosis DNA is required to optimally induce expression of the Zur regulon including the ESX-3 secretion system and multiple alternative ribosome proteins. Thus, ADP-ribosylation of DNA can provide an epigenetic link through every aspect of DNA biology from replication to transcription to translation.

overall_design: M.tuberculosis wild-type and DarT-darG-knockout starins compared with and without the TPEN zinc chelating compound

first: Rachel

last: Butler

first: Schuller

last: Marion

first: Ritu

last: Jaiswal

first: Jayanta

last: Mukhopadhyay

first: Jim

last: Barber

first: Emily

last: Wasson

first: Alex

last: Couto Alves

first: Ivan

last: Ahel


title: Spatial transcriptomics and in situ immune cell profiling of the host ectocervical landscape of HIV infected Kenyan sex working women

city: Stockholm

first: Kristina

last: Broliden

state: Solna

address: Visionsgatan 4, J7:20

department: Dept. of Medicine Solna

country: Sweden

institute: Karolinska Institutet

summary:
Introduction: Chronic immune activation is a hallmark of human immunodeficiency virus (HIV) infection that significantly impacts disease pathogenesis. However, in-depth studies characterizing the immunological landscape of the ectocervix during chronic HIV infection remain scarce despite the importance of this tissue site for HIV transmission.

Methods: Ectocervical tissue samples were obtained from antiretroviral-naïve HIV-seropositive and -seronegative Kenyan female sex workers. Sampeling aimed for the follicular phase of the menstrual cycle. These samples were assessed by spatial transcriptomics and Gene Set Enrichment Analysis. We further performed multi-epitope ligand cartography (MELC) using an in situ staining panel that included 17 markers of primarily T cell–mediated immune responses.

Results: Spatial transcriptomics revealed tissue-wide immune activation encompassing immune responses associated with chronic HIV infection. First, both the epithelial and submucosal compartments showed diverse but significant upregulation of humoral immune responses, as indicated by the expression of several antibody-related genes. Second, an antiviral state–associated cellular immunity was also observed in the HIV-seropositive group, characterized by upregulation of genes involved in interferon signaling across the mucosal tissue and a more spatially restricted mucosal expression of genes related to T cell activity and effector functions relative to the HIV-seronegative group. Additionally, HIV associated structural alterations were evident within both compartments. Downregulated genes across the epithelium were mainly linked to epithelial integrity, with the outer layer involved in terminal differentiation and the inner layer associated with epithelial structure. MELC analysis further revealed a significantly increased ectocervical leukocyte population in HIV-seropositive participants, primarily driven by an increase in CD8+ T cells while the CD4+ T cell population remained stable. Consistent with our spatial transcriptomics data, T cells from HIV-seropositive participants showed an increased effector phenotype, defined by elevated expression of various granzymes.

Conclusion: By combining spatial transcriptomics and MELC, we identified significant HIV-associated cervical immune activity driven by induction of both T and B cell activity, together with a general antiviral state characterized by sustained interferon induction. These findings underscore that chronic HIV infection is associated with an altered ectocervical mucosal immune landscape years after primary infection. This sheds light on HIV pathogenesis at distant local sites and complements current knowledge on HIV-associated systemic immune activation.

overall_design:
In this study we compared gene expression between samples from female sex workers who are living with HIV (HIV group; n=5), and healthy female sex workers (control group; n=5. All of the participants  were in the follicular menstrual stage. Ectocervical tissue were obtained as part of our broader cohort. longitudinal investigation within the Sex Worker Outreach Program in Pumwani, Nairobi, Kenya

***************************************************************
Raw files for human/patient samples were not submitted to GEO due to concerns about submitting personally identifiable sequence data for open access.
***************************************************************


title: A Granulin Variant Causing Childhood Interstitial Lung Disease Responsive to anti-TNF-a Biologic Therapy

first: John

last: Kennedy

address: 300 Longwood Ave, 5th floor

department: Division of Pulmonary Medicine

institute: Boston Children's Hospital/Harvard Medical School

summary: We combined whole exome sequencing with digital spatial mRNA profiling of clinical lung biopsies in the diagnostic evaluation ofapre-teen with progressive idiopathic fibrotic lung and liver disease refractory to standard therapies. The combined findings of homozygosity for the p.Cys139Arg loss-of-function progranulin (GRN) variant and an alveolar macrophage transcriptomic signature consistent with TNF-alpha pathway activation motivated treatment with anti-TNF monoclonal antibodies, resulting in dramatic improvement of her lung and liver disease.  These findings demonstrate the clinical utility of convergent multiomics in the evaluation and treatment of rare disease

overall_design:
Eight FFPE  lung biopsy samples were assembled into an array FFPE block. Immunoflorescence staining was completed for epithelium (PanCK), Macrophages (CD68), Type-2 pneumocytes (ABCA3) and nuclei per GeoMX DSP protocol. Three Regions of interest (ROI) of macrophages within alveoli,  were selected for each sample and whole transcriptome data was retrieved and analysed with Next Generation Sequencing (NGS) readout per GeoMx DSP NGS readout protocol.
The study was designed to compare intra-alveolar macrophages from pediatric Interstitial lung disease samples from children with known monogenic lung disease and histocopies.

first: Benjamin

last: Raby

first: Seung-han

last: Baek


title: Epigenetic control of replication, gene expression and growth phase by ADP-ribosylation of DNA in Mycobacterium tuberculosis [RNAseq_LogStationary]

overall_design: DarTG-KO vs wild-type RNASeq in log and stationary phase.


title: Epigenetic control of replication, gene expression and growth phase by ADP-ribosylation of DNA in Mycobacterium tuberculosis [ADPRseq]

city: Southampton

last: COUTO ALVES

address: 216 Tremona Street

department: School of Human Development and Health

institute: University of Southampton

sample_organism: Mycobacterium tuberculosis variant bovis

overall_design: ADPrSeq, using an antibody reactive to ADP-ribosylated ssDNA to pull-down ADP-ribosylated DNA before identifying enriched sequences by sequencing. ADP-ribosylation was induced by CRISPRi-knockdown of DarG in M. bovis BCG.


title: A detailed analysis of second and third generation sequencing approaches for accurate length determination of short tandem repeats and homopolymers [TypeV_ONT]

first: Yimin

last: SHEN

first: Sophie

last: Jeanjean

last: Shen

first: Lise

last: Hardy

first: Antoine

last: Daunay

first: Marc

last: Delépine

first: Zuzana

last: Gerber

first: Antonio

last: Alberdi

first: Emmanuel

last: Tubacher

first: Jean-François

last: Deleuze

first: Alexandre

last: How-Kit


title: A detailed analysis of second and third generation sequencing approaches for accurate length determination of short tandem repeats and homopolymers [TypeIII_Illumina]


title: IGF2BP3 enhances ferroptosis resistance in colon cancer by stabilizing SLC7A11 mRNA and is regulated by miR-98-5p

status: Public on Feb 21 2025

city: Nanjing

first: Yaya

last: Sun

address: No. 87 Dingjiaqiao, Hunan Road, Gulou District

institute: Southeast University

summary: Colorectal cancer (CRC) is one of the most prevalent malignancies worldwide, with increasing incidence and mortality rates. Resistance to cell death is a hallmark of cancer, and ferroptosis, a form of non-apoptotic cell death, has emerged as a critical factor in tumor suppression. The RNA-binding protein IGF2BP3, which plays a significant role in colon cancer progression, has been shown to modulate various oncogenic processes. However, its involvement in ferroptosis regulation in colon cancer remains largely unexplored. This study investigates the role of IGF2BP3 in ferroptosis regulation and its potential as a therapeutic target in colon cancer. Our data show that IGF2BP3 is upregulated in colon cancer tissues and correlates with poor prognosis. Knockdown of IGF2BP3 in colon cancer cell lines enhances sensitivity to ferroptosis induction, evidenced by increased reactive oxygen species (ROS) and malondialdehyde (MDA) levels, which are reversed by the ferroptosis inhibitor ferrostatin-1. Mechanistically, IGF2BP3 regulates ferroptosis by stabilizing SLC7A11 mRNA, a key ferroptosis regulator, through its interaction with the mRNA. Additionally, miR-98-5p directly targets IGF2BP3, enhancing ferroptosis sensitivity. In vivo studies confirm that IGF2BP3 knockdown suppresses tumor growth, highlighting its potential as a therapeutic target. Overall, our findings suggest that IGF2BP3 plays a pivotal role in regulating ferroptosis in colon cancer, offering new avenues for therapeutic strategies in colon cancer treatment.

overall_design: RNA-seq profiling of three pairs of negative control and IGF2BP3 KD HCT116 cells.

first: Qingwei

last: Liu

first: Junjie

last: Wu

first: Weimin

first: Xin

last: Shi

first: Congxing


title: Spatial Transcriptomic Analysis of Surgical Resection Specimens of Primary Head and Neck Squamous Cell Carcinoma Treated with Afatinib in a Window-of-Opportunity Study (EORTC90111-24111)

status: Public on Feb 23 2025

city: Brussels

first: Jean-Pascal

last: Machiels

address: Avenue Hippocrate 10

institute: Cliniques Universitaires Saint-Luc

summary: Afatinib-induced tumor and microenvironment modifications in head and neck squamous cell carcinoma were evaluated by spatial transcriptomics in surgical specimens and RNA-sequencing in tumor biopsies of patients included in the EORTC-90111-24111 window-of-opportunity study. The aim was to explore tumor evolution and composition under anti-HER therapy. Based on our previous investigations by RNA-seq on tumor biopsies, surgical slides of ID08 & ID15 from the epithelial-to-mesenchymal (EMT)-cluster and ID30 from the non-EMT cluster were investigated with spatial transcriptomics. Dimension reduction in ID30 revealed 14 clusters, with clusters overlapping three tumor nodules and the stroma. Differential expression analysis between tumor nodules showed enrichment of the hallmark EMT genelist, with 123 genes in common between the analyses. These genes were involved in PDGF and MET signaling pathways. By comparing gene expression in paired tumor biopsies and the 123 genes from differential analyses obtained in ID30, a list of 13 genes involved in cancer pathways and EMT emerged which were also highly expressed in ID08 and ID15. These results show a progressive apparition of genes implicated in EMT, MET and PDGF pathways in tumors after afatinib. Notably, a list of 13 genes emerged which may contain targets to prevent tumor evolution after anti-HER therapy.

overall_design: Afatinib-induced tumor and microenvironment modifications in head and neck squamous cell carcinoma were evaluated by spatial transcriptomics in three surgical specimens of patients included in the EORTC-90111-24111 window-of-opportunity study.

first: Simon

last: Beyaert

first: Axelle

last: Loriot

first: Sandra

last: Schmitz


title: The complete molecular atlas of adult C. elegans glia across sexes

city: Seattle

first: Manu

last: Setty

state: WA

address: 1100 Fairview Ave N

department: Basic Sciences Division

institute: Fred Hutchinson Cancer Center

summary: A comprehensive understanding of nervous system function requires molecular insight into the diversity and sex dimorphism of both its component cell types, glia and neurons. Here, we present a single-nuclear RNA sequencing (RNA-seq) census of all neuroectoderm-derived glia in the adult C. elegans nervous system, across sexes. By iteratively coupling computational modeling and custom analytics with in vivo validations, we uncovered molecular markers for all glia, as well as class-specific and pan-glial molecular signatures. These identified that each glia is functionally heterogeneous across the nervous system and variably sex dimorphic between sexes. Thus, this glial transcriptome (wormglia.org) offers deep mechanistic insights into glial biology brain wide. Complementing the existing C. elegans neuronal transcriptome and mapped connectome, it also enables single-cell and molecular resolution insight into the entire nervous system of an adult metazoan.

overall_design:
Single-nuclear RNA-seq of C. elegans glia from hermaphrodite and male animals with the pan-glial promoter PmiR-228 .  Worms were grown on 10 cm, standard 1% NGM agar plates seeded with E.coli strain OP50.  To obtain synchronized day 1 adult worms, we first obtained embryos by performing hypochlorite treatment (1M NaOH + 4% NaOCl freshly made) on adult hermaphrodites. The embryos hatched overnight (16-20 hours) on unseeded NGM agar plates and starved L1 arrested worms were recovered. All male data was acquired in him-5 mutant background. Single nuclei suspensions were obtained after lysing worms. The nuclei were sorted with a Sony SH800S cell sorter fitted with the 100µm nozzle running at a speed of 10-12k events per second using the PE filter set. For the hermaphrodite samples, age matched N2 worms were used as negative control to set FACS gates. For male samples, him-5 males were used as negative controls. The negative controls were taken through identical dissociation protocols. The nuclei were then loaded into a hemocytometer and counted to determine the final concentration. We targeted 10,000 cells per sample and used the 10X Chromium platform using 10X NextGem v3.1 chemistry. cDNA was amplified for 12 cycles and the index PCR was cycled 12 times. Final libraries were brought to 10 nM concentration and processed on an Illumina HiSeq2500 sequencer. Male and hermaphrodite samples were prepared and sequenced on different days, for a total of 2 biological replicates for hermaphrodites and 2 for males.

Please note that both raw and processed data for GSM8092237, GSM8092238 samples have been updated on Jun 25, 2025.

first: Maria

last: Purice

first: Elgene

last: Quitevis

first: R

middle: S

last: Manning

first: Liza

last: Severs

first: Nina-Tuyen

last: Tran

first: Violet

last: Sorrentino

first: Fienan

first: Aakanksha

last: Singhvi


title: crossNN is an explainable framework for cross-platform DNA methylation-based classification of tumors [sequencing-based methylome profiling]

status: Public on Feb 24 2025

city: Berlin

first: Philipp

last: Euskirchen

address: Charitéplatz 1

country: Germany

institute: Charité - Universitätsmedizin Berlin

type: Methylation profiling by high throughput sequencing

summary: DNA methylation-based classification of brain tumors has emerged as a powerful and indispensable diagnostic technique. Initial implementations have used methylation microarrays for data generation, but different sequencing approaches are increasingly used. Most current classifiers, however, rely on a fixed methylation feature space, rendering them incompatible with other platforms, especially different flavors of DNA sequencing. Here, we describe crossNN, a neural network-based machine learning framework which can accurately classify tumor entities using DNA methylation profiles obtained from different platforms and with different epigenome coverage and sequencing depth. It outperforms other deep and conventional machine learning models with respect to diagnostic accuracy and computational requirements while still being fully explainable. We use crossNN to train a pan-cancer classifier to discriminate more than 170 tumor types across all organ sites. Validation in an independent cohort of >5,000 tumors profiled using different microarray and sequencing platforms, including low-pass nanopore and targeted bisulfite sequencing, demonstrates the robustness and scalability of the model with 99.1% and 97.8% precision for brain tumor and pan-cancer model, respectively.

overall_design:
Tumor genomic DNA was subjected to methylation array or sequencing-based methylome profiling. Platform-specific preprocessing was performed as indicated and beta values (microarray) or methylated allele frequencies (all sequencing platforms) were used for classification by crossNN after binarization.

***************************************************************
Raw files for human/patient samples were not submitted to GEO due to concerns about submitting personally identifiable sequence data for open access.
***************************************************************

first: Einar

last: Vik-Mo

first: Skarphedinn

last: Halldorsson

first: Christian

last: Thomas

first: Anne

last: Albers

first: Ulrich

last: Schüller

first: Anton

last: Appelt

first: Regina

last: Reimann

first: Markus

last: Rechsteiner

first: Patrick

last: Harter

first: Katharina

last: Weber

first: Pia

last: Zeiner


title: Genome-wide Association Mapping for Heat Shock Tolerance in Mercenaria mercenaria through SNP Microarray Analysis

city: Stony Brook

first: Denis

last: Grouzdev

address: 100 Nicolls Rd

institute: Stony Brook University

summary: This study aimed to establish a genome-wide association for heat tolerance using the newly developed 66K SNP array for Mercenaria mercenaria. Northern quahogs from three local farms were combined for a heat challenge by increasing temperature at 1°C per day from 24°C to 35°C (Phase I), maintaining at 35°C for two days before decreasing to 27°C within the next 24 hr, then to 24°C within 24 hr. Survival-time analysis showed different survivals among quahogs from these three farms during the heat challenge. Mortality during the temperature increase period (Phase I) was 38, 46, and 55%, and after the temperature decrease was 36, 30, and 29%. For the survivors, no changes were found in body weight before and after the heat shock challenges (p < 0.265). The PCA analyses of SNP frequencies indicated significant genetic differences associated with clam survival under heat stress across the different farms. The fastStructure analysis also revealed the proportions of different ancestral components within the clams, highlighting the genetic factors that may contribute to their varying survival rates under heat stress. The heritability of the heat tolerance traits was 0.680 ± 0.063. GWAS analysis indicated that one SNP exhibited a significant association with the time-to-death trait of northern quahogs and was in chromosome 7. More significant SNPs (p < 10-3.5) were inside genes that have been reported to function in heat tolerance such as serine/threonine-protein kinase 31 and carbohydrate sulfotransferase 11, and some genes found within 50K bp far from SNP sites have a relationship with heat tolerance such as toll-like receptors 4 and 6 (TLRs 4 and TLRs 6), uracil-DNA glycosylase, and a disintegrin and metalloproteinase with thrombospondin motifs gon-1 (ADAMTs). Overall, these findings highlight the power of high-throughput approaches for the identification of superior clam genotypes for further breeding.

overall_design: 633 samples

first: Huiping

last: Yang

first: Zhenwei

last: Wang

first: Jayme

last: Yee

first: Yangqing

last: Zeng

first: Leslie

last: Sturmer

first: Bassem

last: Allam


title: crossNN is an explainable framework for cross-platform DNA methylation-based classification of tumors

first: Philipp

last: Euskirchen

type: Methylation profiling by genome tiling array

overall_design: Tumor genomic DNA was subjected to methylation array or sequencing-based methylome profiling. Platform-specific preprocessing was performed as indicated and beta values (microarray) or methylated allele frequencies (all sequencing platforms) were used for classification by crossNN after binarization.


title: Spatial mapping of transcriptomic and lineage plasticity in metastatic pancreatic cancer

city: New York

first: Anirban

last: Maitra

state: NY

address: Smilow 910, 522 1st Ave

department: Perlmutter Cancer Center

institute: New York University Grossman School of Medicine

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


summary: Patients with treatment-refractory pancreatic cancer often succumb to widespread systemic metastases; however, the transcriptomic heterogeneity that underlies recalcitrance to therapy remains understudied, particularly in the spatial context. We constructed high-resolution spatial maps of transcriptional heterogeneity, clonal architecture and lineage plasticity using spatially resolved transcriptomics from 55 individual samples of primary tumour, liver, lung, and peritoneal metastases, collected from 13 patients via a rapid ("warm") autopsy program. Additionally, we validated the lineage composition and spatial distribution using patient-derived xenograft (PDX) models generated from the primary tumours of two patients.

overall_design: Visium spatial transcriptomics (10X Genomics) was performed on fresh frozen or FFPE tissues. To minimize batch effects, primary and their matched metastatic samples from the same patients were loaded onto the same Visium slide.

first: Guangsheng

last: Pei

first: Jimin

last: Min

first: Kimal

last: Rajapakshe

first: Vittorio

last: Branchi

first: Paola

last: Guerrero

first: Benson

last: Selvanesan

first: Linghua


title: EC-8042 disrupts both the primary SP/KLF transcription regulatory network and the secondary network induced by HDACi treatment.  [H3K27me3 ChIP-seq]

status: Public on Feb 20 2025

city: Tianjin

first: Yu

last: Kong

address: 22nd Qixiangtai Road

institute: Tianjin Medical University

summary: Diffuse intrinsic pontine gliomas (DIPGs) are lethal pediatric brain tumors with limited therapeutic options. Frequently harboring H3K27M mutations, these tumors are resistant to Histone deacetylase inhibitors (HDACi) in clinical trials for yet unclear reasons. Given this, there is a critical need for exploring the reasons of insufficient clinical manifestations of HDACi and identifying effective combinatorial therapeutic strategy for the treatment of DIPG. To explore the possibility of combining HDACi with EC-8042, an analog of Mithramycin that blocks the DNA binding of SP/KLF factors，We performed ChIP-seq of H3K27me3 in SU-DIPG-XVII cells after treated with DMSO, EC-8042, vorinostat and combination vorinostat with EC-8042. And discovered that EC-8042 reverses the activated transcriptional programs caused by HDACi.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for the histone modification H3K27me3 in SU-DIPG-XVII cells after treated with DMSO, EC-8042, vorinostat and combination vorinostat with EC-8042.

first: Xuejiao

last: Lv

first: Yingying

last: Zhao

first: Zhongye

last: Dai

first: Qian

first: Fan


title: PRPS activity governs redox homeostasis in MYC-driven lymphoma

city: Cincinnati

first: John

last: Cunningham

state: OH

address: 3125 Eden Ave

department: Cancer & Cell Biology

institute: University of Cincinnati

summary: Myc hyperactivation coordinately regulates numerous metabolic processes to drive lymphomagenesis. However, the temporal and epistatic relationships between the medley of pathways, factors, and mechanisms that must functionally cooperate to preserve homeostasis in Myc-overexpressing cells remain largely unknown. Here, we characterize the earliest metabolic alterations upon induction of oncogenic Myc and pinpoint the major determinants of redox balance in Myc-overexpressing lymphomas. We find that Myc rapidly stimulates the oxidative pentose phosphate pathway (oxPPP), nucleic acid synthesis, and mitochondrial respiration, which collectively steers cellular equilibrium to a more oxidative state. Acting at the nexus of these processes, we identify Myc-dependent hyperactivation of the phosphoribosyl pyrophosphate synthetase (PRPS) enzyme as the primary regulator of redox status in lymphoma cells. Mechanistically, Myc induces expression of the allosteric feedback refractory PRPS2 isozyme, thereby remodeling the PRPS enzyme complex to a more active state that efficiently funnels ribose-5-phosphate from the PPP to downstream nucleotides. Genetic inactivation of PRPS2 increases oxPPP flux and futile cycling, leading to increased NADPH levels and reductive stress-mediated cell death. Employing a pharmacological screen in wild-type, PRPS1- or PRPS2-knockout lymphoma cells to reveal cooperative functional interactions, we discovered that cells engineered to lack PRPS1 or PRPS2 displayed opposing differential sensitivities to compounds targeting the glutathione and thioredoxin systems, outlining effective rational combinatorial therapeutic approaches in Myc-driven lymphomas. Collectively, our work unravels how the activity of one critical node amongst the expansive metabolic architecture of a cell can be tuned by an oncogenic pathway to alter redox homeostasis and create new exploitable dependencies

overall_design: We first conducted RNA-sequencing on primary murine B lymphocytes isolated from Eμ-Myc transgenic mice compared to WT (C57BL/J6) mice to establish a molecular catalog of Myc-deregulated gene expression programs. We then conducted RNA-sequencing on primary murine B lymphocytes of Eμ-Myc transgenic mice compared to Eμ-Myc; PRPS2 KO mice, to assess if metabolic alterations to redox homeostasis that we observed upon PRPS2 KO interfaced with the Myc-deregulated gene expression program.

first: Austin

last: MacMillan

first: Karmela

middle: R

last: Gertz

first: Juechen

last: Yang


title: Inhibition of SP/KLF transcription regulatory network and histone deacetylases acts synergistically against H3K27M-DIPG

summary: Diffuse intrinsic pontine gliomas (DIPGs), frequently harboring H3K27M mutations, are lethal pediatric brain tumors within no effective treatment. Here our epigenomic analyses uncover a marked enrichment of the SP/KLF transcription factors in open chromatin regions specifically in H3K27M-mutated DIPG cells compared to normal pontine neural progenitor cells. We show that SP1 depletion or inhibition of SP/KLF DNA binding with EC-8042, an optimized Mithramycin analog, significantly suppresses the proliferation and invasiveness of H3K27M-DIPG cells. In a screen of epigenetic drugs, we find that histone deacetylase inhibitors (HDACi) synergize with EC-8042 to suppress H3K27M-DIPG cell growth. The RNA-seq in SU-DIPG-IV and SU-DIPG-XVII cells after treated with DMSO, EC-8042, vorinostat and combination vorinostat with EC-8042 revealed that HDACi activates transcriptional programs that enhance tumor adaptability and invasiveness, an effect counteracted by EC-8042. And EC-8042 in combination with HDACi synergistically represses the expression of cell cycle-associated genes and therefore suppresses H3K27M-DIPG cell proliferation, inhibiting tumor progression in orthotopic xenograft models. Transcriptomic analysis further supports that the combination treatment drives transcriptional programs correlating with favorable prognosis in DIPG patients. Therefore, our regulome profiling in H3K27M-DIPGs has provided mechanistic insights into HDACi resistance and a proof-of-concept for novel targeting therapeutics.

overall_design: RNA-seq in SU-DIPG-IV and SU-DIPG-XVII cells after treated with DMSO, EC-8042, vorinostat and combination vorinostat with EC-8042.

last: Wang


title: EC-8042 disrupts both the primary SP/KLF transcription regulatory network and the secondary network induced by HDACi treatment. [ATAC-seq]

summary: Diffuse intrinsic pontine gliomas (DIPGs), frequently harboring H3K27M mutations, are lethal pediatric brain tumors within no effective treatment. By performing ATAC-seq in human pontine progenitor cells (hPPCs) and H3K27M-mutated DIPG cells, we identified that the DIPG-opened chromatin regions are highly enriched for SP/KLF motifs. We show that SP1 depletion or inhibition of SP/KLF DNA binding with EC-8042, an optimized Mithramycin analog, significantly suppresses the proliferation and invasiveness of H3K27M-DIPG cells. In a screen of epigenetic drugs, we find that histone deacetylase inhibitors (HDACi) synergize with EC-8042 to suppress H3K27M-DIPG cell growth. We then performed ATAC-seq in SU-DIPG-XVII cells after treated with DMSO, EC-8042, vorinostat and combination vorinostat with EC-8042. And discovered that HDACi treatment enhances chromatin accessibility to SP/KLF factors, while EC-8042 disrupts both the primary SP/KLF transcription regulatory network and the secondary network induced by HDACi treatment.

overall_design: Assay for Targeting Accessible-Chromatin with high-throughout sequencing (ATAC-seq) in hPPCs and H3K27M-mutated DIPG cells; ATAC-seq in SU-DIPG-XVII cells after treated with DMSO, EC-8042, vorinostat and combination vorinostat with EC-8042.


title: EC-8042 disrupts both the primary SP/KLF transcription regulatory network and the secondary network induced by HDACi treatment.  [SP1&H3K27me3 CUT&Tag]

summary: Diffuse intrinsic pontine gliomas (DIPGs), frequently harboring H3K27M mutations, are lethal pediatric brain tumors within no effective treatment. The DIPG-opened chromatin regions are proved to be highly enriched for SP/KLF motifs. Using CUT&Tag of SP1 and H3K27me3 in human pontine progenitor cells (hPPCs) and H3K27M-mutated DIPG cells, we detected the gain of SP1 occupancy correlates with the loss of H3K27me3. Here our epigenomic analyses uncover a marked enrichment of the SP/KLF transcription factors in open chromatin regions specifically in H3K27M-mutated DIPG cells compared to normal pontine neural progenitor cells. We show that SP1 depletion or inhibition of SP/KLF DNA binding with EC-8042, an optimized Mithramycin analog, significantly suppresses the proliferation and invasiveness of H3K27M-DIPG cells. In a screen of epigenetic drugs, we find that histone deacetylase inhibitors (HDACi) synergize with EC-8042 to suppress H3K27M-DIPG cell growth. CUT&Tag of SP1 in SU-DIPG-XVII cells after treated with DMSO, EC-8042, vorinostat and combination vorinostat with EC-8042 revealed that HDACi treatment enhances chromatin accessibility to SP/KLF factors, while EC-8042 disrupts both the primary SP/KLF transcription regulatory network and the secondary network induced by HDACi treatment.

overall_design: CUT&Tag of SP1 in SU-DIPG-XVII cells after treated with DMSO, EC-8042,vorinostat and combination vorinostat with EC-8042; CUT&Tag of SP1 and H3K27me3 in hPPC-180606, SU-DIPG-IV, and SU-DIPG-XVII cells.


title: In vivo pulse-chase in C. elegans reveals intestinal histone turnover changes upon starvation

status: Public on Feb 19 2025

city: Indianapolis

first: Scott

middle: T

last: Aoki

state: Indiana

address: 635 Barnhill Drive MS-4071

department: Biochemistry and Molecular Biology

institute: Indiana University School of Medicine

summary: The ability to study protein dynamics and function in the authentic context of a multicellular organism is paramount to better understand biological phenomena in animal health and disease. Pulse-chase of self-labeling tag fusion proteins provide the opportunity to label proteins of interest and track those proteins over time. There are currently several challenges associated with performing in vivo protein pulse-chase in animals, such as cost, reproducibility, and accurate detection methods. The C. elegans model organism has attributes that alleviate many of these challenges. This work tests the feasibility of applying the Halo modified enzyme (HaloTag) for in vivo protein pulse-chase in C. elegans. HaloTag intestinal histone reporters were created in the worm and used to demonstrate that reporter protein could be efficiently pulse-labeled by soaking animals in ligand. Labeled protein stability could be monitored over time by fluorescent confocal microscopy. Further investigation revealed reporter protein stability was dependent on the animal’s nutritional state. ChIP-seq of the reporters showed incorporation in chromatin with little change hours into starvation, implying a lack of chromatin regulation at the time point tested. Collectively, this work presents a straightforward method to label and track proteins of interest in C. elegans that can address a multitude of biological questions surrounding protein stability and dynamics in this animal model.

overall_design: ChIP-seq on intestine-specific his-58/H2B and his-9/H3.1 reporter protein from his-58/H2B or his-9/H3.1 C. elegans reporter strains. N2 (WT) was included as an ChIP negative control.  his-58/H2B and his-9/H3.1 reporter strains were either fed or starved prior to ChIP-seq processing.

first: Christopher

last: Borchers

first: Hyun

last: Roh


title: scRNAseq gene expression and VDJ-TCR analysis of PBMCs from patients with tattoo uveitis and sarcoidosis

city: Acton

first: Zhi-Ping

last: Feng

state: ACT

address:
131 Garran Road, John Curtin School Of Medical Research Building (Level 3, Stage 1)
, The Australian National University

country: Australia

institute: JCSMR

summary: To elucidate the complexity of immune responses in the formation of granuloma, we performed the single-cell RNA-sequencing analysis. PBMCs derived from tattoo uveitis patients in both active and inactive stages and sarcoidosis patients were collected to characterize their similarities and difference. PBMCs from age-matched healthy donors were considered as controls.

overall_design: Sorted live PBMCs were prepared two patients with active tattoo uveitis, three patients with convalescent tattoo uveitis, three patients with sarcoidosis and three age-match healthy donors. Single-cell gene expression and TCR VDJ libraries were prepared by Chromium Next GEM Single Cell 5' Kit v2 Dual Index and Single Cell Human TCR Amplification Kit (10x Genomics) with the help from Biomolecular Resource Facility at ANU. Libraries were then sequenced on NovaSeq 6000 sequencer (Illumina) with 2 x 50 bp paired-end reads. 10X Cell Ranger (10X Genomics, v6.0.1) was utilized to align the reads to the human genome (GRCh38-2020-A) using default parameters.

first: Yuwei

last: Hao

first: Anthea

last: Anantharajah

first: Matthew

last: Cook


title: A spatiotemporal cell atlas of cardiopulmonary progenitor cell allocation during development

city: Philadelphia

first: Sylvia

last: Michki

address: 3615 Civic Center Blvd

department: Pulmonary & Sleep Medicine

institute: Children's Hospital of Philadelphia

summary: The mesoderm surrounding both the developing heart and anterior foregut endoderm provides instructive cues guiding lung development and serves as a source of cardiopulmonary mesodermal progenitor cells (CPPs) expressing Wnt2 that give rise to both cardiac inflow tract and lung mesodermal cell lineages. To assess mechanisms of Wnt2+ CPP contribution to heart and lung development, we performed single cell RNA sequencing (scRNA-seq) on lineage-traced cells labeled at E8.5 and collected their progeny across the developmental lifespan.

overall_design: Wnt2-CreERT2 was used to drive lineage expression of EYFP. Lung and heart cells positive for EYFP were isolated by FACS at multiple developmental timepoints.

first: Hongbo

last: Wen

first: Prashant

last: Chandrasekaran

first: Annabelle

last: Jin

first: Josh

last: Pankin

first: Minqi

last: Lu

first: Derek

last: Liberti

first: Jarod

last: Zepp

first: Raja

last: Jain

first: David

middle: B

last: Frank


title: ZC3HC1 has functions distinct from TPR and is dispensable for TPR localization to the nuclear basket

status: Public on Feb 18 2025

city: Edinburgh

first: Bethany

last: Bartlett

address: Crewe Road South

institute: University of Edinburgh

summary: Background: The nuclear basket is a ‘fishtrap’-like structure on the nucleoplasmic face of the nuclear pore complex which has been implicated in diverse functions including RNA export, heterochromatin organisation, and mitosis. Recently, a novel component of the nuclear basket, ZC3HC1, has been described. The localisation of ZC3HC1 to nuclear pores has been reported to occur reciprocally with TPR, a major structural component of the nuclear basket. Methods and Results: Using immunofluorescence and RNA sequencing, here we show that in human fibroblasts, although ZC3HC1 localisation to nuclear pores is TPR-dependent, TPR localises to pores regardless of the presence of ZC3HC1. We demonstrate that knockdown of TPR and ZC3HC1 produce distinct transcriptional profiles. Conclusions: Our results suggest that there is little overlap in function between these two nuclear basket proteins

overall_design: RNA-seq profiling of IMR90 cells treated with either siCTRL or siZC3HC1 for 3 days.

first: Wendy

last: Bickmore


title: Targeting PIKfyve-driven lipid homeostasis as a metabolic vulnerability in pancreatic cancer [CRISPR screen]

city: Ann Arbor

first: Brian

last: Magnuson

state: MI

address: 1500 East Medical Center Drive

institute: University of Michigan

summary: Pancreatic ductal adenocarcinoma (PDAC) subsists in a nutrient-deregulated microenvironment, making it particularly susceptible to treatments that interfere with cancer metabolism. For example, PDAC utilizes and is dependent on high levels of autophagy and other lysosomal processes. Although targeting these pathways has shown potential in preclinical studies, progress has been hampered by the challenge of identifying and characterizing favorable targets for drug development6. Here, we characterize PIKfyve, a lipid kinase integral to lysosomal functioning, as a novel and targetable vulnerability in PDAC. In human patient and murine PDAC samples, we discovered that PIKFYVE is overexpressed in PDAC cells compared to adjacent normal cells. Employing a genetically engineered mouse model, we established the essential role of PIKfyve in PDAC progression. Further, through comprehensive metabolic analyses, we found that PIKfyve inhibition obligated PDAC to upregulate de novo lipid synthesis and specifically sphingolipid synthesis, a relationship previously undescribed. PIKfyve inhibition triggered a distinct lipogenic gene expression and metabolic program, creating a dependency on de novo lipid metabolism pathways, by upregulating genes such as FASN and ACACA. In PDAC, the KRAS-MAPK signaling pathway is a primary driver of de novo lipid synthesis, specifically enhancing FASN and ACACA levels. Accordingly, the simultaneous targeting of PIKfyve and KRAS-MAPK resulted in the elimination of tumor burden in a syngeneic orthotopic model and tumor regression in a xenograft model of PDAC. Taken together, these studies suggest that disrupting lipid metabolism through PIKfyve inhibition induces synthetic lethality in conjunction with KRAS-MAPK-directed therapies for PDAC.

overall_design: Human PDAC cells (MIA PaCa-2) were transduced with a pooled gRNA library (Addgene #110066).  After selection, cells treated with apilimod for 17 days were harvested for a CRISPR screen.

first: Caleb

last: Cheng

first: Nicholas

middle: J

last: Rossiter

first: Yuanyuan

last: Qiao

first: Arul

last: Chinnaiyan

first: Costas

last: Lyssiotis


title: Targeting PIKfyve-driven lipid homeostasis as a metabolic vulnerability in pancreatic cancer [ChIP-seq]

overall_design: Chromatin immunoprecipitation of c-Myc in human PDAC cells (MIA PaCa-2).  Cells were treated with DMSO, AMG510, or Trametinib and DNA extracted by ChIP-seq using anti-Myc antibodies (all 3 treatments) or IgG (DMSO treatment only).  Four samples were prepared and sequenced in total.

first: Tongchen

last: He


title: Targeting PIKfyve-driven lipid homeostasis as a metabolic vulnerability in pancreatic cancer

overall_design: Refer to individual Series


title: Single-cell transcriptome of myeloid progenitor populations from the mouse bone marrow

city: Hangzhou

first: Sheng

last: Pan

address: #866 Yuhangtang Road

institute: Zhejiang University

summary: Various types of myeloid cells play a universal and vital role in maintaining homeostasis and immune responses in vertebrates. However, the development of myeloid lineage diversity remain elusive. Here, we constructed a single-cell transcriptional map of myeloid progenitors from the mouse bone marrow, in order to dicepher the ontogeny of myeloid lineage diversity. The profiled myeloid progenitor samples include LMPP, CMP and three biological replicates of GMP.

overall_design: LMPP (Lin-c-Kit+Sca-1+CD34+Flt3+), CMP (Lin-c-Kit+Sca1-CD34+CD16/32low), and three biological replicates of GMP (Lin-c-Kit+Sca-1-CD34+CD16/32high) samples from the bone marrow of Balb/C mice were isolated and transcriptionally profiled by scRNA-seq (10x Genomics).

first: Haoyu

last: Tang

first: Bingpeng

last: Yao


title: hnRNPL phase separation activates PIK3CB transcription and promotes glycolysis in ovarian cancer (hnRNPL RNAseq)

status: Public on Feb 14 2025

city: Chongqing

first: Qinlv

last: Wei

state: Chongqing

address: Chongqing

institute: Children’s Hospital of Chongqing Medical University

summary: Ovarian cancer has the highest mortality rate among gynecologic tumors worldwide, with unclear underlying mechanisms of pathogenesis. RNA-binding proteins (RBPs) primarily direct post-transcriptional regulation through modulating RNA metabolism. Recent evidence demonstrates that RBPs are also implicated in transcriptional control. However, the role and mechanism of RBP-mediated transcriptional regulation in tumorigenesis remain largely unexplored. Here, we show that the RBP heterogeneous ribonucleoprotein L (hnRNPL) interacts with chromatin and regulates gene transcription by forming phase-separated condensates in ovarian cancer. hnRNPL phase separation activates PIK3CB transcription and glycolysis, thus promoting ovarian cancer progression. Notably, we observe that the PIK3CB promoter is transcribed to produce a non-coding RNA which interacts with hnRNPL and promotes hnRNPL condensation. Furthermore, hnRNPL is significantly amplified in ovarian cancer, and its high expression predicts poor prognosis for ovarian cancer patients. By using cell-derived xenograft and patient-derived organoid models, we show that hnRNPL knockdown suppresses ovarian tumorigenesis. Together, our study reveals that phase separation of the chromatin-associated RBP hnRNPL promotes PIK3CB transcription and glycolysis to facilitate tumorigenesis in ovarian cancer. The formed hnRNPL-PIK3CB-AKT axis depending on phase separation can serve as a potential therapeutic target for ovarian cancer.

overall_design: RNAseq of hnRNPL in OVCAR3 cells

first: Qinglv

first: Tao

last: Liu

first: Ping

last: Yi


title: Studies of Human Erythropoiesis Using classic 2D liquid culture and 3D scaffolds

status: Public on Feb 17 2025

city: Milan

first: Santo

last: Diprima

address: Via Olgettina 58

department: COSR

country: Italy

institute: San Raffaele Hospital

summary: Different bioengineering techniques have been developed to enable the production of erythrocytes in vitro. However, extrapolating the 3D structure and function of erythroblastic islands remains challenging. In our research, we employ a comprehensive strategy emphasizing physiological red blood cell (RBC) differentiation using a bespoke cocktail of cytokines and nutrients, including transferrin. The system was cultured for up to three weeks with hematopoietic stem and progenitor cells (HSPCs) in three-dimensional (3D) scaffolds engineered to mimic the physical and chemical properties of human bone marrow. Within the scaffold, HSPCs undergo erythroblastic maturation within the first 2 weeks of culture. After 3 weeks, fully mature CD36⁻ CD71⁻ CD235a⁺ erythrocytes can be observed, accompanied by increased hemoglobin synthesis. In the 3D culture, diverse stages of erythroblast maturation are observed, driven by the activation of autophagy, which facilitates organelle clearance and membrane remodeling. This process leads to reduced surface integrin expression and significantly enhances RBC enucleation. Our findings underscore the importance of a 3D environment in supporting RBC maturation.

overall_design: Bulk RNA-seq profiling of 2D and 3D cultures during erythroid differentiation. Differentiation is carried out in vitro.

first: Alessandra

last: Balduini

first: Christian

last: Di Buduo

first: Francesca

last: Careddu


title: hnRNPL phase separation activates PIK3CB transcription and promotes glycolysis in ovarian cancer (RNApolII ChIPseq)

status: Public on Feb 13 2025

overall_design: ChIPseq of RNApolII in OVCAR3 cells


title: hnRNPL phase separation activates PIK3CB transcription and promotes glycolysis in ovarian cancer (hnRNPL ChIPseq)

overall_design: ChIPseq of hnRNPL in OVCAR3 cells


title: Maternal intra-epithelial lymphocytes support lactogenesis and offspring fitness

city: BETHESDA

first: Cihan

last: Oguz

state: MD

address: NIHBC 29B BG RM 1NN20, 9000 ROCKVILLE PIKE

institute: NIH

summary: Breastfeeding is an obligatory requirement of mammalian survival. This fundamental process is associated with the remodeling of maternal physiology including the transformation of mammary gland into milk-secreting organ. While adaptive immunity has been associated with the broad control of host physiology, how maternal immunity contributes to organismal remodeling during pregnancy including mammary gland remodeling and function remains largely unknown. Here, we show that maternal adaptive immunity plays a critical role in shaping lactogenesis. Specifically, physiological adaptation to pregnancy is associated with thymic involution and paradoxical enrichment in intraepithelial lymphocyte precursors that no longer migrate to the gut but preferentially accumulate within the mammary gland. Within this compartment the precursors develop as T-bet expressing lymphocytes accumulating within the mammary epithelium in an IL-15 dependent manner. Mammary intra-epithelial lymphocytes control milk production by favoring differentiation of both contractile and milk-secreting cells, thereby affecting offspring fitness. Altogether, this work uncovers a previously unappreciated contribution of the maternal adaptive immune system in organismal remodeling during pregnancy associated with mammary gland development and function.

overall_design: To identify whether mammary unconventional intra-epithelial lymphocytes regulate mammary epithelial and basal cell differentiation, we performed scRNA-seq on mammary epithelial-myoepithelial and lymphoid cells along with bulk RNA-Seq on CD8 beta+ T-cells and DN (double negative) NK1.1+ lymphocytes in mice. The number of libraries sequenced is one for mammary epithelial-myoepithelial scRNA-seq, four for lymphoid scRNA-seq, three for each of the bulk RNA-Seq samples derived from CD8 beta+ T-cells and DN NK1.1+ lymphocytes. The scRNA-seq libraries were coupled with hashtag oligo (HTO) libraries for labeling the samples in order to demultiplex the pooled RNA libraries into individual mice for downstream analysis, whereas the lymphoid cells were also used for generating T cell receptor (VDJ region) sequencing libraries for characterizing the immune repertoire landscape.

first: Dan

last: Corral

first: Daniel

last: Yong

first: Liang

last: Chi

first: Jeremie

last: Delaleu

first: Andrea

last: Pichler

first: Katharine

last: Yang

first: Verena

last: Link

first: Olena

last: Kamenyeva

first: Juraj

last: Kabat

first: Eduard

last: Ansaldo

first: Jia

last: Nie

first: Lilian

last: Sun

first: Florent

last: Ginhoux

first: Remy

last: Bosselut

first: Yasmine

last: Belkaid


title: Activity-dependent development of the body's touch receptors

status: Public on Feb 12 2025

city: Boston

first: Celine

last: Santiago

state: Massachusetts

address: 210 Longwood Ave

department: Neurobiology

institute: Harvard Medical School

summary: We report a role for activity in the development of the primary sensory neurons that detect touch. Genetic deletion of Piezo2, the principal mechanosensitive ion channel in somatosensory neurons, caused profound changes in the formation of mechanosensory end organ structures. Peripheral nervous system specific deletion of the voltage-gated sodium channel Nav1.6 (Scn8a), which resulted in altered electrophysiological responses to mechanical stimuli, also disrupted somatosensory neuron morphologies, supporting a role for neuronal activity in end organ formation. Single cell RNA sequencing of Piezo2 mutants revealed changes in gene expression in the sensory neurons activated by light mechanical forces, whereas other neuronal classes were minimally affected, and genetic deletion of Piezo2-dependent genes partially reproduced the defects in mechanosensory neuron structures observed in Piezo2 mutants. These findings indicate that mechanically evoked neuronal activity acts early in life to shape the maturation of mechanosensory end organs that underlie our sense of gentle touch.

overall_design: Dorsal root ganglia from segmental levels C2 and below were dissected and dissociated to obtain neurons for single cell RNA sequencing analysis. In the first bioreplicate, DRG from two Cdx2-Cre/+; Piezo2flox/flox animals (age P24) were dissected and assigned as “Mutant sample 1” and DRG from three control littermates were dissected on the same day and assigned as “Control sample 1.” In the second bioreplicate, DRG from three Cdx2-Cre/+; Piezo2flox/flox animals (age P21) were dissected and assigned as “Mutant sample 2” and DRG from two control littermates were dissected and assigned as “Control sample 2.”

first: Nikhil

last: Sharma

first: David

middle: D

last: Ginty


title: The myoblast methylome: Multiple types of associations with chromatin and transcription

city: Ipswich

first: Sriharsa

last: Pradhan

state: MA

address: 240 County Road

institute: New England Biolabs

summary: Epigenetic changes are implicated in repair and physiological responses of postnatal skeletal muscle (SkM) as well as in prenatal embryogenesis. This study examined the epigenomics and transcriptomics of human myoblasts (SkM progenitor cells) vs. those of diverse other cell and tissue types from both global genomic and single-gene perspectives. Using enzymatic methyl-seq (EM-seq) and whole-genome bisulfite sequencing (WGBS) of myoblast DNA and available WGBS profiles of other cell cultures, we determined myoblast differentially methylated regions (DMRs). We also examined several DMRs in reporter gene assays. Among the unusual findings was the positive association of promoter-adjacent hypermethylation in myoblasts with transcription turn-on for some genes (e.g., SIM2 and TWIST1), but at down-modulated levels. In contrast, some genes, like the brain-specific OLIG2, were silent and embedded in repressed chromatin in myoblasts and many diverse cell populations but displayed myoblast-specific hypermethylated promoters. OLIG2 exhibited binding of the myogenic MYOD transcription factor in its vicinity. One OLIG2-downstream MYOD+ site overlapped enhancer chromatin in myotubes. These findings suggest that OLIG2 silencing only by repressive chromatin is insufficient in myoblasts without the addition of DNA hypermethylation. The numerous hypomethylated DMRs at enhancer chromatin in myoblasts were bound by MYOD much more frequently than by CTCF. Combined with previous studies, our results suggest a more prevalent role for MYOD than for CTCF in organizing transcription-enhancing chromatin interactions at hypomethylated regions. We also found that myoblast-hypomethylated enhancer chromatin enriched in H3K36me3 was much more likely to be associated with genes preferentially expressed in myoblasts than were such regions without H3K36me3 enrichment. Therefore, there may be a special role in gene upregulation for the regional combination of DNA hypomethylation with H3K27ac, H3K4me1, and H3K36me3 enrichment. The unusual relationships between epigenetics and gene expression that we observed need further study in the SkM lineage to better understand fine-tuning of muscle differentiation and diseases.

overall_design: DNA was purified from non-transformed myoblast primary cultures derived from quadriceps biopsies of control individuals (Tsumagari et al., 2013), namely, CM1 (42-year-old female), CM3 (46-year-old male), and CM6 (45-year-old male). Cell cultures had been carefully generated and passaged in collaboration with Rabi Tawil (Tsumagari et al., 2011). Each batch of myoblasts used for DNA methylation analysis was checked for >90% purity by desmin immunostaining because fibroblast-like contaminating cells can easily outgrow myoblasts and give misleading methylome results (Chandra et al. 2015). WGBS was performed on CM3 using standard protocols (Chen F, Zhang G, et al. 2016). Methylation profiling of CM3, CM1, and CM6 was done using enzymatic methyl-seq (EM-seq) (Vaisvila et al. 2021). This process involved enzymatic oxidation of 5mC and 5hmC (by TET2), providing protection from further deamination by APOBEC3A while unmethylated cytosine are deaminated to uracil. Briefly, 0.2 µg of DNA was used to prepare EM-seq libraries in duplicate. The libraries were then cleaned using NEBNext® sample selection beads, pooled, and diluted to 1.5 nM for sequencing on a NovaSeq 6000(Illumina).

first: Chaithanya

last: Ponnaluri

first: Pierre-Olivier

last: Estève

first: Melanie

last: Ehrlich

first: Sagnik

last: Sen


title: Anti-tumor CD4Th1 cells controls the migration and outgrowth of disseminated cancer cells II

city: Tampa

first: Brian

last: Czerniecki

state: FL

address: 12902 Magnolia Drive

department: Breast Oncology

institute: Moffitt Cancer Center

summary: Comparison of gene expression profiles of disseminated cancer cells with primary tumors and metastatic tumors

overall_design: To investigate the gene expression profiles of disseminated cancer cells compared to primary tumors and metastatic tumors in breast cancer and role of anti-tumor CD4Th1 immune response on the gene expression profiles, we performed RNA sequencing.

first: Ganesan

last: Ramamoorthi