title: Role of endothelial STING1 in the transcriptional response to LPS

summary: RNA-seq analysis of kidney endothelium and whole kidney from mice 15 hours after an intraperitoneal challenge with 250 micrograms of LPS per mouse.

overall_design: Four groups: WT+Saline, WT+LPS, STINGiEKO+Saline, STINGiEKO+LPS


title: ASNA1 CKO with XMCL-CRE+ E14.5 mouse heart RNAseq

status: Public on Aug 10 2025

city: San Diego

first: Zengming

last: Zhang

address: 9500 Gilman Drive, La Jolla

country: USA

institute: UCSD

type: Expression profiling by high throughput sequencing

summary: ASNA1 (also known as TRC40) is a key component of the tail-anchored (TA) protein targeting pathway. To investigate its role in the heart, we generated cardiomyocyte-specific ASNA1 conditional knockout (ASNA1 CKO) mice. RNA-seq analysis was performed on E14.5 embryonic heart to identify transcriptional changes caused by ASNA1 deficiency. Our results reveal that ASNA1 is essential for maintaining the stability of TA proteins and regulating vesicular transport in cardiomyocytes, which are critical for normal cardiac development and function.

overall_design: To investigate the role of Asna1 in cardiac development, we generated cardiomyocyte-specific Asna1 knockout mice (Asna1^fl/fl; Xmlc2-Cre^+/−) by crossing floxed Asna1 mice with Xmlc2-Cre transgenic mice. Ventricular tissues were collected from embryonic day 14.5 (E14.5) knockout and control littermates (n = 4 biological replicates per genotype). Total RNA was extracted, and RNA integrity was assessed prior to library preparation. Strand-specific mRNA libraries were prepared using the Illumina TruSeq Stranded mRNA kit and sequenced on the Illumina HiSeq 6000 platform to generate ~30 million paired-end reads (150 bp) per sample.

first: Ju

last: Chen


title: Single-cell gene expression of a glioma cell line (GL261) cultured adherently or as neurospheres

status: Public on Aug 18 2025

city: Caldwell

first: Richard

middle: Luke

last: Daniels

state: ID

address: 2112 Cleveland Blvd

department: Biology

institute: The College of Idaho

summary:
GL261 cells are a widely-used model system for glioma tumors and can be cultured adherently or as free-floating cell aggregates known as neurospheres. Neurospheres can be implanted into mice where they readily form tumors. This suggests that neurospheres may more closely resemble the in-vivo tumor phenotype. Our study has two primary objectives: 1) To determine differences in gene expression between adherent cells and the tumor-forming neurospheres and 2) To determine the extent of homogeneity in these cell populations.

This project was supported by an Institutional Development Award (IDeA) from the National Institute of General Medical Sciences of the National Institutes of Health (Grant #P20GM103408) along with a Murdock College Science Research Program Grant (SR-202119904) from the M.J. Murdock Charitable Trust.

overall_design: GL261 cells were cultured adherently in DMEM with 10% FBS and 1% penicillin-streptomycin. Adherent cells were trypsinzed, collected from culture flasks, and analyzed using scRNA-Seq. Neurosphere formation was induced with the addition of epidermal growth factor (EGF, 20 ng / ml), fibroblast growth factor (FGF, 20 ng / ml) and B-27 (1:50) to the culture media. Neurospheres were collected after 12 days, trypsinized, and analyzed using scRNA-Seq.

first: Emily

middle: A

last: Freko

first: Colton

middle: E

last: Troxel

first: Ruby

last: Olvera

middle: L


title: Polycomb Repressive-Deubiquitinase Complex Safeguards Oocyte Epigenome and Female Fertility by Restraining Polycomb Activity [CUT&RUN]

status: Public on Aug 13 2025

city: Cincinnati

first: Zhiyuan

state: Ohio

address: 3333 Burnet Avenue

institute: Cincinnati Children's Hospital Medical Center

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Polycomb group proteins are essential for oogenesis, yet mechanisms underlying the non-canonical Polycomb landscapes in oocytes remain unclear. Here we report BAP1, a core component of the Polycomb Repressive-Deubiquitinase (PR-DUB) complex, as a key negative regulator of Polycomb activity during oogenesis. BAP1 restricts pervasive H2AK119ub1 accumulation in oocytes and protects oocyte-specific broad H3K27ac, particularly within gene-poor regions, from ectopic H3K27me3 deposition. While PR-DUB has been linked to gene repression, in oocytes BAP1 primarily promotes transcription and contributes minimally to Polycomb-mediated silencing. BAP1-deficient oocytes cannot support preimplantation development due to impaired maternal-to-zygotic transition and defective embryonic enhancer activation. Notably, aberrant H3K27me3 landscape established in BAP1-null oocytes persists into early embryos. Together, these findings reveal a critical role for PR-DUB in safeguarding the oocyte epigenome by protecting euchromatin from ectopic Polycomb activity, rather than enforcing transcriptional repression.

overall_design: This study is to investigate how loss of BAP1 may impact transcriptome and chromatin states of mouse oocytes and early embryos. Total RNA-seq and H2AK119ub1/H3K27me3/H3K27ac CUT&RUN were performed for control (Bap1 flox/flox) and conditional KO (Gdf9-iCre, Bap1 flox/flox) fully grown oocytes. The control and conditional KO oocytes were fertilized with wild type sperm, resulting control and maternal KO embryos. Total RNA-seq were performed for control and maternal KO embryos at late 1-cell, early 2-cell, and late 2-cell stages. PolyA RNA-seq were performed for control and maternal KO groups for embryonic day 6.5 epiblast (EPI), visceral endoderm (VE), and extra-embryonic ectoderm (EXE). H3K27me3/H3K27ac CUT&RUN were performed for both groups at late 2-cell stage. H3K27me3 CUT&RUN were performed for both groups for morulae, E6.5 EPI, VE, and EXE.

first: Jinwen

last: Kang

first: Peiyao

last: Liu

first: Shoko

last: Ichimura

first: Lauryn

last: Cook

first: Mengwen

last: Hu

first: Satoshi

last: Namekawa


title: The PIK3CA/AKT pathway drives therapy resistance in rhabdomyosarcoma

status: Public on Aug 08 2025

city: Charlestown

first: David

last: Langenau

state: MA

department: Molecular Pathology

institute: Massachusetts General Hospital

summary: Olaparib and temozolomide (OT) combination therapy is in clinical trial evaluation foradolescent rhabdomyosarcoma (RMS) muscle cancers. Unfortunately, resistance to OT hasbeen reported in other cancers, with no counterstrategies available. Using preclinical mousexenograft experiments, we show that OT is effective at curbing RMS growth, yet a subset oftumors develop resistance that is associated with transcriptomic changes that occur in theabsence of recurrent genomic mutation. Importantly, a majority of resistant RMS modelsupregulate the PIK3CA/AKT pathway, which in turn activates NRF2 transcription factorphosphorylation and subsequent transcriptional expression of multidrug resistance ABCtransport proteins that rapidly efflux drugs from cells. We found that the PIK3CA inhibitoralpelisib re-sensitized resistant tumor cells to OT therapy by suppressing the expression of ABCtransport proteins. Excitingly, RMS use the same PIK3CA/AKT pathway activation to driveresistance to standard-of-care combination therapy vincristine, actinomycin D, andcyclophosphamide (VAC) and the combination of OT + alpelisib effectively killed VAC-resistantRMS. Alpelisib also re-sensitized resistant RMS to chemotherapy in preclinical xenograft mousemodels resulting in reduced tumor burden and extended disease-free survival. Our work definesa common resistance pathway in RMS and has credentialled a new preclinical strategy to killtherapy resistant RMS.

overall_design: Single cells were dissociated by tumor dissociation kit from PDX tumor on NSG mice and analyzed using scRNAseq.

first: Qiqi

last: Yang

first: Qian

last: Qin


title: FcγR-targeted tuftsin clusters rejuvenate macrophages in preclinical sepsis–associated secondary infection

city: Beijing

first: Qing

last: Guangchao

address: No. 11, First North Road, Zhongguancun, Beijing, 100190, P.R. China

country: China

institute: National Center for Nanoscience and Technology

summary: Sepsis-associated secondary infection often leads to high mortality rate. Dysfunctional macrophages are the primary contributors to inadequate antimicrobial defense in patients   with sepsis-associated immunosuppression, elevating the risk of opportunistic infections. Here, a bacteria-targeted transformable macrophage nanorejuvenator, designated as BATMAN, is developed to effectively tackle sepsis-associated secondary infection by coordinating the arrest of invasive bacteria and rejuvenation of dysfunctional macrophages based on the in situ responsive transformation. The results affirm the BATMAN’s effective binding and transformation on bacterial surface. The enzymatic removal of Chems by bacterial lipase disrupts the hydrophilic-hydrophobic balance of BATMAN, triggering the inside-out rearrangement that exposes the concealed tuftsin and facilitates its assembly into polyvalent peptide clusters on trapped bacteria driven by the assembly of FFVLK. This transformation not only reduces the invasiveness of bacteria, but enhances the interaction between tuftsin clusters and macrophage Fc gamma receptor, promoting bacterial phagocytosis and driving macrophage repolarization. As a result, BATMAN rejuvenates the compromised immune response to eliminate the polymicrobial- and even multidrug-resistant pathogen-induced pulmonary infection in septic mice. Consequently, we anticipate that our in situ transformable BATMAN holds promise as a therapeutic alternative for sepsis-associated secondary infection.

overall_design: RNA-seq profiling of M2 bone marrow-derived macrophages treated with PBS or SA@BATMAN5 for 24 hours

first: Guangchao

last: Qing

first: Yuxuan

first: Xing-Jie

last: Liang

first: Yang

last: Luo


title: Gene regulatory mechanisms guiding bifurcation of inhibitory and excitatory neuron lineages in the anterior brainstem

status: Public on Aug 07 2025

city: Helsinki

first: Sami

last: Kilpinen

address: Viikinkaari 9

department: Faculty of Biological and Environmental Sciences

country: Finland

institute: University of Helsinki

summary: Selector transcription factors control choices of alternative cellular fates during development. The ventral rhombomere 1 of the embryonic brainstem produces neuronal precursors that can differentiate into either inhibitory GABAergic or excitatory glutamatergic neurons important for the control of behaviour. Transcription factors (TFs) Tal1, Gata2 and Gata3 are required for adopting the GABAergic neuronal identity and inhibiting the glutamatergic identity. Here, we asked how these selector TFs are activated and how they control the identity of the developing brainstem neurons. We addressed these questions by analysing chromatin accessibility at putative gene regulatory elements active during GABAergic and glutamatergic neuron lineage bifurcation, combined with studies of transcription factor expression and DNA-binding. Our results show that the Tal1, Gata2 and Gata3 genes are activated by highly similar mechanisms, with connections to regional patterning, neurogenic cell cycle exit and general course of neuronal differentiation. After activation, Tal1, Gata2 and Gata3 are linked by auto- and cross-regulation as well as regulatory interactions with transcription factors of the glutamatergic branch. Predicted targets of these selector TFs include genes expressed in GABAergic neurons, glutamatergic neurons, or both. Unlike genes specific to the glutamatergic branch, the genes expressed in GABAergic neurons appear to be under combinatorial control of Tal1, Gata2 and Gata3.

overall_design: CUT&Tag analysis of the DNA interaction of selected transcription factors (Tal1, Gata2, Gata3, Vsx2, Ebf1, Insm1, Tead2) in E12.5 mouse anterior hindbrain (rhombomere 1)

first: Kaia

last: Achim

first: Juha

last: Partanen


title: R-spondin 2 suppresses hepatic steatosis via activation of AMPK-ACC signaling

city: Memphis

first: Bhupesh

last: Singla

state: TN

address: 881 Madison Ave

institute: UNIVERSITY OF TENNESSEE HEALTH SCI CTR

summary: Metabolic dysfunction-associated steatotic liver disease (MASLD) primarily results from dysregulated lipid metabolism in hepatocytes. However, the mechanisms governing hepatic lipid metabolism remain incompletely understood. Our preliminary experiments demonstrated elevated expression of R-spondin 2 (RSPO2), a matricellular protein, in steatotic livers. To investigate the role of RSPO2 in MASLD and the potential mechanisms involved, we performed bulk RNA sequencing of liver samples from Apoe knockout mice injected with either control Gfp-AAV or Rspo2-AAV to induce RSPO2 overexpression, following 12 weeks of Western diet feeding.

overall_design: Total RNA from Gfp-AAV- or Rspo2-AAV-injected mice liver samples was isolated using TRIzol reagent according to the manufacturer's instructions. The quality of RNA was determined using the Agilent 2100 Bioanalyzer System. The samples with RNA Integrity Numbers of more than 8 were sent to Novogene Corporation Inc., Sacramento, for bulk RNA-sequencing.

first: Ravi

middle: V

last: Aithabathula


title: Fate mapping of peripherally derived macrophages reveals a long-lasting engrafted population that maintains a distinct transcriptomic profile for up to 8 months after Traumatic Brain Injury III

status: Public on Aug 06 2025

city: Redwood City

first: Susanna

last: Rosi

state: CA

address: 2200 Island Dr

institute: Altos Labs

summary: Traumatic Brain Injury (TBI) is one of the most established environmental risk factors for the development of dementia and long term neurological deficits representing a critical health problem for our society. It is well-established that TBI-induced neuroinflammation contributes to the long-lasting cognitive deficits and engages brain-resident macrophages (microglia) as well as monocytes-derived macrophages (MDMs) recruited from the periphery. While numerous studies have characterized microglia response to TBI, and the critical role of early infiltrated MDMs in the development of cognitive dysfunctions, the fate of MDMs in TBI remains unknown. Microglia and MDMs have distinct embryological origins and it is unclear if MDMs can fully transition to microglia after infiltrating the brain. This gap in knowledge is due to the fact that after brain engraftment, MDMs stop expressing their signature markers, thus making discrimination from resident microglia cells elusive. Here, for the first time, we longitudinally trace the fate of MDMs by taking advantage of two complementary yet distinct fate mapping mouse lines, CCR2-creERT2 and Ms4a3-cre, where inflammatory monocytes are permanently labeled even after in situ reprogramming. We demonstrated that early infiltrated MDMs persist in the brain for up to 8 months after TBI in adult female and male mice. Notably, MDMs retain their phagocytic activity while remaining transcriptomically distinct from microglia, and show a signature associated with aging and disease. Our data significantly advance the understanding of long-lasting MDMs and provide critical knowledge for developing more targeted therapeutic interventions for myeloid cells.

overall_design: RNA-seq profiling of peripheral monocytes, and microglia and monocyte-derived macrophages (MDMs) collected from whole brains of Ms4a3-cre::Ai14D mice at 7 and 30 days with and without traumatic brain injury (TBI).

first: Maria Serena

last: Paladini

first: Benjamin

first: Xi

last: Feng

first: Elma

middle: S

last: Frias

first: Karen

last: Krukowski

first: Rene

last: Sit

first: Maurizio

last: Morri

first: Wendy

last: Lam

first: Valentina

last: Pedoia

first: Stefka

last: Tyanova


title: Polycomb Repressive-Deubiquitinase Complex Safeguards Oocyte Epigenome and Female Fertility by Restraining Polycomb Activity [RNA-Seq]

first: Zhiyuan

last: Chen

first: Jinwen

last: Kang

first: Peiyao

last: Liu

first: Shoko

last: Ichimura

first: Lauryn

last: Cook

first: Mengwen

last: Hu

first: Satoshi

last: Namekawa


title: Modification of fat mass through targeting distal enhancer of Ptrf

city: cehngsu

first: zhang

last: songling

state: China

address: wenjianqu

institute: Sichuan Agricultural University, Chengdu 611130, China

summary: We revealed a close positive relationship between Ptrf transcription and adipose mass in mice, and single-nucleus transcriptomics indicated the involment of impariment of adipogenic differentiation, adipocyte metabolism, transportation of multiple nutrients and altered regulatory network in Ptrf knockout-induced decrease of fat mass.

overall_design: We analyzed inguinal white adipose from 6-month-old WT and PTRF KO mice using single-nucleus sequencing.

first: Yu

last: Zhang

first: Keren

last: Long

first: Songling

first: Ziqi

last: Li


title: Fate mapping of peripherally derived macrophages reveals a long-lasting engrafted population that maintains a distinct transcriptomic profile for up to 8 months after Traumatic Brain Injury II

first: Susanna

last: Rosi

overall_design: RNA-seq profiling of monocyte-derived macrophages (MDMs) collected from whole brains of Ccr2-creERT2::Ai14D mice at 7 and 30 days after traumatic brain injury (TBI).

first: Maria Serena

last: Paladini

first: Benjamin

last: Yang

first: Xi

last: Feng

first: Elma

last: Frias

first: Karen

last: Krukowski

first: Rene


title: Fate mapping of peripherally derived macrophages reveals a long-lasting engrafted population that maintains a distinct transcriptomic profile for up to 8 months after Traumatic Brain Injury I

overall_design: RNA-seq profiling of microglia and monocyte-derived macrophages (MDMs) collected from whole brains of Ccr2-creERT2::Ai14D mice at 8 months with and without traumatic brain injury (TBI).

last: Sit

first: Maurizio

last: Morri

first: Wendy

last: Lam

first: Valentina

last: Pedoia

first: Stefka

last: Tyanova


title: Spatial Transcriptomic Profiling of the Mouse Adrenal Gland and Adjacent Adipose Tissue

city: Poznan

first: Marcin

last: Rucinski

address: Swiecicki 6

department: Histology and Embryology

country: Poland

institute: Poznan University of Medical Sciences

summary: This study employs spatial transcriptomics to map the molecular landscape of the mouse adrenal gland, focusing on distinct cortical zones (zona glomerulosa, zona fasciculata, X-zone) and the adrenal medulla, as well as adjacent adipose tissue. Using Visium CytAssist technology, we analyzed adrenal sections from male CD-1® IGS mice, identifying seven distinct cell clusters, including brown and white adipose tissues.

overall_design: Four sexually mature male CD-1® IGS mice, 10 weeks old with a body weight of approximately 37 g were used in this study.  Mice were housed in colony cages in a pathogen-free environment with temperature maintained at 21-23°C and relative humidity between 55-60% and under a 12h light/12 h dark cycle. All mice were given standard chow and water ad libitum. The mice were euthanized by decapitation and the harvested adrenals were immediately preserved in 10% buffered formalin for further analysis.

first: Małgorzata

last: Blatkiewicz

first: Szymon

last: Hryhorowicz

first: Marta

last: Szyszka

first: Joanna

last: Suszyńska-Zajczyk

first: Andrzej

last: Pławski

first: Adam

last: Plewiński

first: Andrea

last: Porzionato

first: Ludwik K.

last: Malendowicz


title: Selective inhibition of BRAF and CRAF sensitizes NF1-deficient malignant peripheral nerve sheath tumors to MEK inhibitors

status: Public on Aug 01 2025

city: Select

first: Angelina

middle: V.

last: Vaseva

state: Oregon

address: Pediatrics

institute: Oregon Health Science University

summary: Background: Treatment for patients with malignant peripheral nerve sheath tumors (MPNST) is an unmet clinical need. Loss of NF1 in MPNST leads to hyperactivation of RAS oncoproteins, however little is known about relevant downstream oncogenic signaling and effective targeted therapies in MPNST are still lacking. Methods: Conditional gene expression, CRISPR-CAS9, and shRNA-mediated knockdown were used to perform gain/loss-of-function experiments to explore the effect of reconstituting the GTPase-activating protein-related domain of NF1 or knockdown of A/B/CRAF kinases on ERK signaling output and MPNST cell growth. Colony formation, cell proliferation and live cells imaging assays were performed to assess cell growth in response to genetic manipulations or drug treatments. Pathway enrichment analysis on RNA sequencing following drug perturbation, efficacy studies in cell-line-derived and patient-derived xenograft models, and immunoblotting/immunohistochemistry were conducted to assess tumor growth and ERK pathway activity in cells or in pharmacodynamic analyses of tumor xenografts. Results: NF1 loss activates RAS/ERK signaling through B/CRAF, and cell growth and ERK signaling of NF1-MPNST are dependent on B/CRAF, but not ARAF. Genetic or pharmacological inhibition of B/CRAF using paralog-selective RAF inhibitor (RAFi) significantly potentiates MEK inhibitor (MEKi) treatment through more effective suppression of ERK signaling and proliferation. This is shown in multiple traditional and patient-derived cell line and xenograft models, including those with acquired resistance to MEKi.

overall_design: Malignant Peripheral Nerve Sheath Tumor (MPNST) cell lines were treated with MEK inhibitor trametinib, BRAF/CRAF inhibitor LXH254, or the combination of both for 48hours. RNA sequencing was then performed and gene expression analysis was done from 3 cell lines.

first: Siyuan

last: Zheng

first: Funan

last: He


title: Fate mapping of peripherally derived macrophages reveals a long-lasting engrafted population that maintains a distinct transcriptomic profile for up to 8 months after Traumatic Brain Injury IV

first: Susanna

last: Rosi

overall_design: Single-nucleus RNA-seq of brain samples from human patients with and without TBI.

first: Maria Serena

last: Paladini

first: Benjamin

last: Yang

first: Xi

last: Feng

first: Elma

last: Frias

first: Karen

last: Krukowski

first: Rene

last: Sit

first: Marco

last: Colonna

first: Amber

last: Nolan


title: Transcriptome Data from Root Tissues of the 'Sakonnakorn' Mulberry Cultivar

status: Public on Aug 03 2025

city: Bangkok

first: Apidet

last: Rakpenthai

state: Chatuchak

address: 50 Ngamwongwan Rd

country: Thailand

institute: Kasetsart University

summary: We employed RNA-seq to profile the transcriptome of Morus 'Sakonnakorn', a cultivar known for its rich secondary metabolite profile. This analysis aimed to elucidate the genetic regulation of the phenylpropanoid pathway and other related metabolic networks in response to specific elicitors.

overall_design: This study utilized 2.5-month-old stem cuttings of Morus ‘Sakonnakorn’, which were propagated aeroponically from a one-year-old parent plant. The experiment involved two treatment groups: one receiving medium molecular weight chitosan (CHI) and another grown in a nitrogen-deficient (-N) medium. A third, untreated group served as the control. For each condition, three biological replicates were maintained.

first: Mutsumi

last: Watanabe

first: Sutkhet

last: Nakasathien


title: The conserved SEN1 DNA/RNA helicase has multiple functions during yeast meiosis

city: Stony Brook

first: Nancy

last: Hollingsworth

state: NY

address: 306 Life Sciences Building

department: Biochemistry and Cell Biology

institute: Stony Brook University

summary: Diploid Saccharomyces cerevisiae cells undergo meiosis when they are starved of nitrogen in the presence of a non-fermentable carbon source. Nutrient starvation triggers expression of Ime1, a master regulatory protein required to activate transcription of meiotic “early genes” that mediate premeiotic S phase and Prophase I processes, including recombination and chromosome synapsis. During prophase, the highly conserved, topisomerase-like protein, Spo11, generates ~200 double strand breaks that are used to identify homologous chromosomes and generate crossovers between them. DNA-RNA hybrids are formed when an RNA molecule anneals to a complementary strand of DNA and are present at the ends of double strand breaks during Prophase I of meiosis in a variety of organisms. One way of removing DNA/RNA hybrids is degradation of the RNA by RNase H. Phenotypic characterization of organisms lacking RNase H activity has demonstrated that regulation of the level of DNA-RNA hybrids is important for meiotic double strand break repair. Sen1 is an essential 5’-3’ DNA-RNA helicase that can remove DNA-RNA hybrids by unwinding the RNA. Sen1 is orthologous to the mammalian Senataxin (SETX) helicase. Mouse mutants lacking either Senataxin or RNase H activity exhibit male infertility and defects in double strand break repair. SETX is also required for meiotic sex chromosome inactivation, making it unclear whether SETX’s role in meiotic recombination is direct or an indirect consequence due to defects in SETX functions that affect transcription. Using a variety of orthogonal approaches, this work demonstrates that SEN1 has multiple, temporally distinct functions that promote yeast meiosis. First, it enables the timely expression of IME1-regulated early genes. Second, it helps prevent/remove DNA-RNA hybrids that form during premeiotic S phase. Third, it facilitates repair of Spo11 double strand breaks generated during Prophase I, as well as chromosome synapsis.

overall_design: RNA was extacted from SEN1 and sen1-md yeast (Saccharomyces cerevisiae) cells using the Qiagen RNeasy kit  at different times after the onset of meiosis.  Sequencing libraries were generated from enriched PolyA RNA using NEBNext Ultra RNA Library kit and analyzed by Illumina paired end sequencing.

first: Robert

last: Gaglione

first: Jonathan

last: Caradonna

first: Ed

last: Luk

first: Amy

last: MacQueen


title: Th17 Cells with Regulatory Phenotype are the Main IL-17F and IL-26 Producers in Palmoplantar Pustulosis

city: Ann Arbor

first: Poulami

last: Dey

address: 1301 Catherine St

institute: Michigan Medicine

summary: Palmoplantar pustulosis (PPP) is a chronic inflammatory skin disorder marked by erythematous pustules and desquamation on the palms and soles. While IL-17 pathways are implicated in PPP, IL-17 blockers have shown modest efficacy, underscoring the need for a deeper understanding of IL-17 involvement. To dissect the cellular and spatial architecture of PPP, we performed single-cell RNA sequencing (scRNA-seq) on lesional, nonlesional, and healthy acral skin to examine cellular composition, transcriptomic profiles, and cell-cell interactions. Unbiased clustering revealed nine major cell types, including an inflammatory keratinocyte subset enriched in IL-17A/TNF signatures and marked by high IL-36G expression. Within the lymphocyte compartment, we identified a hybrid “regTh17” population co-expressing regulatory markers (FOXP3, CTLA4, TIGIT), IL17F, and IL26. This regTh17 subset was distinguished by elevated IL1R1 and CD39, suggesting a IL-1β–driven differentiation. Spatial analyses demonstrated significant neighborhood enrichment of regTh17 cells with IL-36G⁺ supraspinous keratinocytes. RegTh17 cells were the predominant source of IL-17F and IL-26 signals, whereas keratinocytes were predicted as their main receivers. We further observed regTh17 co-expressing TNFRSF4 (OX40) and TNFRSF18 (GITR) specifically at sites of IL36G+ keratinocyte interactions, implicating these pathways in amplification of the IL-17/IL-36 inflammatory loop. Together, our integrated single-cell and spatial profiling uncovers Th17 plasticity in PPP, identifies a regTh17-keratinocyte interaction and highlights IL-17F, IL-26, OX40/OX40L, and GITR/GITRL as candidate targets for precision therapies in this challenging disease.

overall_design: 4-mm lesional and non-lesional punch biopsies were collected from the acral skin of three patients with palmoplantar pustulosis (PPP) and five healthy controls. Single-cell suspensions were prepared and processed using the 10X Genomics Chromium system, followed by sequencing on an Illumina NovaSeq 6000 platform. Raw reads were aligned to the human reference genome (hg38) using Cell Ranger. Downstream analysis included quality control filtering, removal of ambient RNA contamination (SoupX), doublet detection (scDblFinder), data normalization, and batch correction (Harmony) before clustering with Seurat (v5.0.2).

first: Johann

last: Gudjonsson

first: Lam

middle: C

last: Tsoi


title: Therapeutically targeting perivascular macrophage effector function improves CD8+ T-cell infiltration and response to chemotherapeutic drugs in cancer [CD206+LYVE-1+]

city: London

first: James

middle: N

last: Arnold

address: New Hunt’s House, Great Maze Pond

department: Cancer and Pharmaceutical Sciences

country: United Kingdom

institute: King's College London

summary: The tumor microenvironment (TME) plays a crucial role in cancer progression and represents an appealing target for cancer treatment. Tumor-associated macrophages (TAMs) are an abundant stromal cell type in the TME and, due to their plasticity, TAMs can be exploited to promote a pro-tumoral response. TAMs have been implicated in facilitating a variety of pro-tumoral pathways including resistance to anti-cancer therapeutics, immune suppression, angiogenesis, and metastasis. However, pan-TAM depleting approaches have not delivered robust clinical outcomes as single agents. This might be explained due to their non-selective targeting of both pro- and anti-tumoral macrophage subsets. As such, therapeutically targeting key pro-tumoral TAM subsets may be a more desirable and efficacious strategy. Our group has recently characterised a subpopulation of pro-angiogenic and immune-suppressive TAMs which can be identified by their expression of the lymphatic vessel endothelial hyaluronan receptor-1 (LYVE-1). LYVE-1+ TAMs reside spatially proximal to blood vasculature and adopt a collaborative multi-cellular ‘nest’ arrangement which supports their biological activity. LYVE-1+ TAMs selectively express high levels of the immunomodulatory enzyme heme oxygenase-1 (HO-1), an enzyme which catabolizes heme to generate the biologically active catabolites carbon monoxide (CO), biliverdin and ferrous iron. Genetic inactivation of HO-1 in LYVE-1+ TAMs improve anti-tumor CD8+ T-cell infiltration into the TME and enhances the immune-stimulating effects of chemotherapy, resulting in sustain control of tumor growth in a spontaneous MMTV-PyMT murine model of breast cancer. This highlights that HO-1 represents a key effector pathway of these cells that prevents immune-elimination of tumors. Considering translation of these observations, unfortunately, current HO-1 inhibitors are not orally bioavailable, which limits their utility for chronic diseases, such as cancer, where daily administration would be required. In response to this hurdle, we developed a next generation HO-1 inhibitor called KCL-HO-1i. We demonstrate in pharmacokinetic studies that KCL-HO-1i is orally bioavailable in murine models with a serum half-life of around 3hours. Furthermore, oral delivery of KCL-HO-1i alongside standard of care chemotherapy delivers durable tumor control in MMTV-PyMT mice. We have characterised the response of the TME to KCL-HO-1i using flow cytometry, immunofluorescence and RNA sequencing approaches and demonstrate that KCL-HO-1i targeting perivascular LYVE-1+ TAM function supports a broader switch from an immunological ‘cold’ to ‘hot’ TME which provides a more favourable immune landscape for improving the response to chemotherapeutic drugs. Taken together, our data support the use of KCL-HO-1i as novel immunotherapeutic for targeting the function of perivascular TAMs in cancer.

overall_design: 6 MMTV-PyMT mice were divided in 2 treatment groups with 3 mice each group and were treated either with the Vehicle or KCL-HO-1i inhibitor. Tumours have been harvested and digested into single-cell supensions. Then, the cells have been sorted in order to get 5000 cells  CD206+LYVE-1+ for each condition.

first: Meriem

last: Bahri

first: Jit

last: Sarkar


title: Long-chain fatty acid β-oxidation regulates embryonic development by H3K18 acetylation in mice [RNA-seq]

city: 温州

first: kefan

last: zheng

address: 瓯海区茶山街道温州医科大学

institute: wenzhou medical university

summary: Fatty acids are not only important as energy sources, but also playing crucial roles in maintaining cellular homeostasis.Inhibition of long-chain fatty acid β-oxidation (LCFAO) results in preimplantation developmental arrest, downregulated expressions of S phase-related genes, and loss of H3K18ac modification. By profiling the landscape of H3K18ac, we show that H3K18ac is enriched on the promoter regions of S phase-related genes and correlates with their expression. Taken together, we demonstrate that LCFAO could regulate mouse preimplantation development by H3K18ac, providing new evidence for metabolic-epigenetic crosstalk in regulating embryonic development.

overall_design: RNA-seq analysis of mouse 8-cell and morula embryos in both control and TMZ inhibitor-treated groups.

first: Qingran

last: Kong

first: Hao

last: Li

first: Qi

last: Zhao

first: Kefan

last: Zheng

first: Hongdi

last: Cui

first: Entong

last: Song


title: Long-chain fatty acid β-oxidation regulates embryonic development by H3K18 acetylation in mice [CUT&Tag]

status: Public on Aug 05 2025

address: 瓯海区茶山街道温州医科大学

overall_design: Examination of H3K27ac in mouse 8-cell and morula embryos in both control and TMZ inhibitor-treated groups.


title: A Microcavity-Based Sarcoma Spheroid Model for Drug Efficacy and Mechanism Analysis Using Cost-effective 3D Printing Technology

status: Public on Aug 04 2025

city: CLEVELAND

first: Yuan

last: Gao

state: OH

address: 2109 Adelbert Rd., Wood Building Research Tower 300-7, Wood Building Research Tower 300-7

department: Pharmacology

institute: Case Western Reserve University

summary: Ewing sarcoma is a pediatric bone cancer with poor survival in relapsed cases, highlighting the need for better preclinical models. Here, we developed a scalable 3D spheroid platform using SLA-printed microcavity arrays to generate uniform Ewing sarcoma spheroids. High-throughput screening of 11 compounds identified Torin 2, Talazoparib, and Trabectedin as potent inhibitors. Incorporating lung fibroblasts into hybrid spheroids revealed fibroblast-induced drug resistance, mimicking the metastatic tumor microenvironment. Transcriptomic analysis identified activation of NF-κB and TGF-β signaling pathways as key mediators of this resistance. This platform offers a cost-effective, biologically relevant system for drug testing and mechanistic studies in Ewing sarcoma and other stromal-influenced cancers.

overall_design: Hybrid or monoculture spheroids were digested into single cells using trypsin. GFP positive Ewing sarcoma cells were sorted using BD Symphony S6 (CWRU Cytometry & Imaging Microscopy Core), and subject to total RNA extraction using TRIzol according to the manufacturer’s instructions. 250ng of total RNA was used to construct RNA-seq library using the NEBNext UltraExpress RNA Library Prep Kit following manufacturer’s instructions. Briefly, RNA was polyA enriched using NEBNext Poly(A) mRNA Magnetic Isolation Module  and enzymatically fragmented. cDNA was synthesized followed by end repair and adapter ligation, and PCR enrichment with indexed primers. Library was pair end sequenced for 76bp using Illumina NovaSeq platform. Sequencing reads were mapped to reference genome hg38 using RNA STAR with default parameters. Read count tables were created using FeatureCounts with a custom GTF file containing protein coding genes only. Differentially expressed genes were analyzed using DESeq2 with two independent replicates using default parameters. TPM values was calculated using Kallisto.

first: Chao

last: Ma

first: Jaehun

last: Lee

first: Muyi

last: Ye


title: Two transcription factors and one antisense RNA underlie the thermoregulated insect pathogenicity of Yersinia entomophaga MH96

city: Christchurch

first: Amber

middle: Rose

last: Paulson

address: Lincoln Research Centre, Cnr Springs Road And Gerald Street, Private Bag 4749

department: Forage Science

country: New Zealand

institute: AgResearch Litmited

summary: Yersinia entomophaga MH96 is a highly virulent entomopathogen that infects pest insects of economic importance. We discovered a new regulator, Yen6, which influences the virulence of MH96 in Galleria mellonella at 37 ˚C. Yen6 is directly upstream of the yen7 gene, which encodes for a RoeA-like PhoB-containing regulator and that is directly upstream of the Yen Toxin component (Yen-Tc) genes. We found that yen6 is the most temperature-responsive gene in MH96, producing both messenger RNA and non-coding RNA in its 3' untranslated region (UTR). Yen6 encodes a unique LytTR-containing transcription factor that targets sugar uptake genes and an RNA-binding protein. Of interest, the non-coding RNA from the yen6 3’ UTR overlaps with yen7 in the opposite orientation. Deleting yen6 did not significantly affect the transcriptional activity of yen7 or downstream Yen-Tc genes during infection at 37 ˚C. However, when we deleted the yen6 locus or induced yen6 plus a 478-bp region of its 3’ UTR at 25 ˚C, we observed a significant increase in the transcription/ translation rates of the Yen-Tc gene chi1 using a chi1:lacZ fusion. Our findings reveal a novel mode of virulence regulation in MH96, where the yen6 gene exerts control over multiple genes involved in G. mellonella infection and exhibits potential for dual functionality at both transcriptional and translational levels.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Yersinia entomophaga wild-type (MH96) and a mutant deficient for the yen6 gene (PL78_03730). This study also combines data from transcriptome series under GEO accession: GSE142509.

middle: R

first: Maureen

last: O'Callaghan

first: Xue-Xian

last: Zhang

first: Naran

last: Naren

first: Marion

last: Schoof

first: Mark R

middle: H

last: Hurst


title: HSPA1A can alleviate CFA-induced inflammatory pain by modulating macrophages

status: Public on Jul 31 2025

city: Guangzhou

first: Wenjie

address: Guangzhou Medical University, No.1 Xinzao Road, Panyu District

department: School of Basic Medical Sciences

institute: Guangzhou Medical University

summary: Current clinical approaches for managing inflammatory pain are frequently accompanied by adverse effects, significantly compromising patients' quality of life. This study investigates the analgesic potential of murine HSPA1A protein administration in alleviating Complete Freund’s Adjuvant (CFA)-induced inflammatory pain. Findings indicate that HSPA1A mitigates CFA-induced mechanical allodynia positively correlated with macrophage abundance. Transcriptomic RNA sequencing suggests involvement of inflammation-associated pathways in plantar tissues after HSPA1A injection.

overall_design: This study investigates the analgesic potential of murine HSPA1A protein administration in alleviating Complete Freund’s Adjuvant (CFA)-induced inflammatory pain.Plantar tissues from HSPA1A-treated and control mice were collected.

first: Feiyu

last: Chen


title: A-to-I editing and adr mutant gene expression in C. elegans germlines

city: BLOOMINGTON

first: Emily

middle: Ann

last: Erdmann

state: IN

address: 1001 E Third Street

institute: Indiana University

summary: In this study, we performed high-throughput RNA-seq on young adult germline samples from wild-type and adr-2(-) C. elegans hermaphrodites. A-to-I editing sites were identified using SAILOR. Differential gene expression analysis was performed using DESeq2.

overall_design: Germlines were isolated from synchronized young adult C. elegans hermaphrodites raised at 20 degrees C. Strains used include N2 and BB20 (adr-2(ok735)). RNA was extracted and poly-A selection was performed prior to library preparation.

first: Heather

last: Hundley


title: The impact of mab_1638 on the M. abscessus transcriptome [ChIP-seq]

status: Public on Jul 30 2025

city: Worcester

first: Scarlet

last: Shell

state: Massachusetts

address: 60 Prescott St, WPI

department: Biology and Biotechnology

institute: Worcester Polytechnic Institute

summary: Mycobacterium abscessus is a major human pathogen, mostly infecting people with pre-existing pathological lung conditions such as cystic fibrosis. Only little is known about the ways M. abscessus regulates its virulence factors and pathogenesis phenotypes. The production of glycopeptidolipids (GPL) is a major determinant of virulence of this bacterium, with clinical isolates that lack GPL synthesis and export generally exhibiting more aggressive clinical behavior. The current paradigm is that GPL production is abolished in vivo via irreversible, spontaneous mutations taking place as part of in-host evolution. Little is known about the mechanisms or extent to which GPL production may be regulated. We have found an unusual TetR-like transcription factor of M. abscessus, mab_1638, identified via screening of a comprehensive transposon-mutant library, that appears to be a strong positive regulator of the entire GPL biosynthesis and export gene cluster through a combination of direct and indirect mechanisms. The inactivation of mab_1638 by a transposon led to stable and visually obvious rough colony morphology, as well as increased virulence in infection models, characteristic of rough, non-GPL-producers. Transcriptome analysis found the mab_1638:tn mutant to have 118 differentially expressed genes, including the GPL locus. It appears mab_1638 encodes an unusual TetR transcription factor required for  the production of GPL in M. abscessus and therefore having a profound effect on virulence traits. This finding raises the important possibility that M. abscessus strains appearing smooth in laboratory growth conditions may nonetheless downregulate GPL-cluster genes in other conditions and thus acquire the phenotypic characteristics of rough strains.

overall_design: ChIP-seq was performed with an anti-HA antibody on four strains: (1) WT M. abscessus ATCC19977; (2) M. abscessus ATCC19977 transformed with a construct encoding an HA-tagged M. tuberculosis protein (mmaA2) not expected to bind DNA; (3) M. abscessus ATCC19977 with a transposon disrupting the gene mab_1638 (mab_1638::tn) and transformed with a construct encoding MAB_1638 with an N-terminal HA tag; and (4) mab_1638::tn transformed with a construct encoding MAB_1638 with an C-terminal HA tag.

first: Daniel

last: Barkan

first: Michal

last: Bar-Oz

first: Junpei

last: Xiao

last: Meir

first: Manitosh

last: Pandey

first: Stefan

last: Oehlers


title: Retinoic acid-regulated epigenetic marks identify Alx1 as a direct target gene required for optic cup formation [ChIP-seq]

city: La Jolla

first: Gregg

last: Duester

address: 10901 North Torrey Pines Road

department: Center for Cardiovascular and Muscular Diseases

institute: Sanford Burnham Prebys Medical Discovery Institute

summary: Retinoic acid (RA) is a transcriptional control agent that regulates several aspects of eye development including invagination of the optic vesicle to form the optic cup, although a target gene for this role has not been previously identified. As loss of RA synthesis in Rdh10 knockout embryos affects the expression levels of thousands of genes, a different approach is needed to identity genes that are directly regulated by RA. Here, we combined ChIP-seq for epigenetic marks with RNA-seq on eye tissue from wild-type embryos and Rdh10-/- embryos that exhibit failure in optic cup formation. We identified a small number of genes with decreased expression when RA is absent that also have decreased presence of a nearby epigenetic gene activation mark (H3K27ac). One such gene was Alx1 that also has an RA response element (RARE) located near the RA-regulated H3K27ac mark, providing strong evidence that RA directly activates Alx1. In situ hybridization studies showed that Rdh10-/- embryos exhibit a large decrease in eye Alx1 expression. CRISPR/Cas9 knockout of Alx1 resulted in a failure in optic cup formation, thus demonstrating that RA directly activates Alx1 in order to stimulate this stage of eye development.

overall_design: H3K27ac ChIP-seq of WT and Rdh10 KO mouse embryonic craniofacial tissue

first: Marie

last: Berenguer


title: Lysine-specific demethylase 6B promotes STAT1-mediated macrophages activation during atherosclerosis development

city: hangzhou

first: huan

last: chen

state: Zhejiang

address: Hangzhou, Zhejiang Province, China

institute: Zhejiang Chinese Medical University

summary: Atherosclerosis (AS) induced coronary heart disease is still the first killer threatening human health due to high morbidity and mortality. How N6-methyladenosine modification (m6A) in macrophage participates in atherosclerosis progression is still completely unclear. In this study, by performing meRIP-seq in macrophages during differentiation and activation processes, we aim to understand the landscape of m6A spectrum in macrophage from different stages. Moreover, we also find a large class of histone methylation modification enzymes were regulated by m6A modification. Western blot, qPCR and ChIP-seq results demonstrate m6A modification regulates Lysine-specific demethylase 6B (Kdm6b)-dependent macrophage activation. In mechanism, Kdm6b interacts and methylates Jak1 inducing its phosphorylation-mediated macrophage activation. Furthermore, RIP-qPCR detection indicates following macrophage differentiation and activation, both m6A writers Mettl3 and Rbm15 participates in m6A modification of Kdm6b mRNA. Finally, by performing atherosclerotic model on macrophage-specific Kdm6b knockout mice on Ldlr-/- background, we demonstrate Kdm6b promotes macrophage activation-mediated atherosclerosis by amplifying inflammation and destabilizing plaque. This study will provide a new understanding of the pathogenesis of AS and is expected to develop a new target for the treatment of AS.

overall_design: Comparative gene expression profiling analysis of RNA-seq data: Effects of GSKJ1 and IFNγ on genes in mouse bone marrow-derived macrophages


title: The histone-methyltransferase DOT1L cooperates with LSD1 to control cell division in blast-phase MPN [ChIP-seq]

status: Public on Jul 29 2025

city: Hannover

first: Florian

last: Perner

address: Carl-Neuberg-Str. 1

department: Hematology, Hemostasis, Oncology and Stem Cell Transplantation

country: Germany

institute: Hannover Medical School

summary: Persistence of JAK2-mutated clones that may undergo clonal evolution and malignant transformation remains a challenge in myeloproliferative neoplasms (MPN), Novel therapeutic approaches to attenuate clonal evolution and progression to blast-phase are therefore urgently needed. LSD1 (KDM1A) inhibitors reduce symptoms and clonal burden in MPN, but whether these compounds may be effective in advanced disease stages remained so far elusive. Using a chromatin-focused CRISPR-Cas9 screen, we identified the histone methyltransferase DOT1L as a synthetic lethal target under pharmacologic LSD1 inhibition. DOT1L knockout impaired cellular fitness, reduced proliferation, and prolonged survival in xenografts. Furthermore, genetic inactivation of DOT1L increased LSD1 inhibitor sensitivity up to 100-fold resulting in cell cycle arrest and apoptosis induction in TP53 mutant blast-phase MPN. Mechanistically, we have identified a novel, non-canonical function of DOT1L which co-occupied LSD1-bound enhancers and contributed to the repression of transcriptional programs independent of its enzymatic activity. DOT1L loss cooperated with LSD1 inhibitors to activate tumor suppressive programs, while pharmacologic inhibition of DOT1Ls catalytic activity failed to elicit comparable effects. These findings indicate that leveraging DOT1L targeting via protein degradation or RNA interference, rather than conventional enzymatic inhibition, could enhance the therapeutic efficacy of LSD1 inhibitors in blast-phase MPN.

overall_design: ChIP sequencing of DOT1L, LSD1, H3K79me2 and H3K4me1 in different cell lines (HEL, SET2, MOLM13) and primary MPN-BP patient samples.


title: The histone-methyltransferase DOT1L cooperates with LSD1 to control cell division in blast-phase MPN [RNA-seq]

overall_design: 1. RNAseq of Human Erythroleukemia cells (HEL cell line) with a CRISPR-Cas9-mediated knockout of DOT1L (or non-targeting control) treated with the LSD1-inhibitor Bomedemstat for 24h and 5d. 2. RNAseq of MPN-BP primary patient sample with a shRNA-mediated knockdown of DOT1L (or scrambled control) cultured in methylcellulose for 7 days under puromycine selection for shRNA-expressing cells.


title: Microarray Expression Analysis of Circular RNA in Perineural Invasion of Pancreatic Ductal Adenocarcinoma

first: Rufu

address: No. 106, Zhongshan 2nd Road, Guangzhou

institute: Guangdong Provincial People's Hospital

type: Non-coding RNA profiling by high throughput sequencing

summary: This study aimed to investigate the expression profile of circular RNAs (circRNAs) in pancreatic cancer and evaluate their potential as reliable biomarkers and novel diagnostic and therapeutic targets, with a specific focus on molecular characteristics associated with perineural invasion. We employed Arraystar Human circRNA Array Analysis to detect circRNA expression levels in 3 pancreatic cancer tissues with perineural invasion and 3 pancreatic cancer tissues without perineural invasion. The results revealed significant differences in circRNA expression between the two groups, with distinctly different expression patterns observed in the samples. This study analyzed the expression profile of circRNAs and their potential value as reliable biomarkers and potential novel diagnostic and therapeutic targets for pancreatic cancer, particularly in the context of perineural invasion.

overall_design: To clarify the exact mechanism of circular RNAs (circRNAs) in the process of perineural invasion in pancreatic cancer, total RNA was extracted from 3 pancreatic cancer tissues with perineural invasion and 3 pancreatic cancer tissues without perineural invasion in this study. Next-generation sequencing was performed to explore the differences in circRNA expression profiles between the two groups.


title: Identification of candidate long non-coding RNAs and mRNAs associated with heart aging in mice

city: Shanghai

first: Zheng

last: Kuai

address: No180 fenglin Road

institute: Zhongshan Hospital Fudan University

type:
Expression profiling by array
Non-coding RNA profiling by array

summary: To further development of our gene expression approach to aging, we have employed lncRNA/mRNA microarray expression profiling as a discovery platform to identify genes with the potential to distinguish cardiac aging. We collected hearts from 3-month-old and naturally aged 20-month-old mice, respectively. Age-related differentially expressed lncRNAs and mRNAs were obtained by the method of RNA sequencing microarray of mouse heart tissue.

overall_design: Age induced gene expression was measured in 3-month-old mouse heart and 20-month-old mouse heart . Five independent experiments were performed at each group（3m and 20m） using different donors for each experiment.

first: Yu

last: Hu


title: I-SPY2 TRIAL RPPA data for ganitumab arm (and control arm)

city: San Francisco

first: Denise

middle: M

last: Wolf

address: 2340 Sutter st

institute: University of California, San Francisco

summary: Pre-treatment specimens from patients treated on the I-SPY2 neoadjuvant breast cancer trial were studied to identify predictive biomarkers associated with response to the regimen of paclitaxel, an anti-type I IGF receptor (IGF-1R) antibody ganitumab, and metformin (PGM) followed by doxorubicin and cyclophosphamide (AC) compared to control therapy (paclitaxel followed by AC). This record contains protein/phosphoprotein data from pre-treatment laser capture microdissected (LCM) tumor biopsies for up to 162 key signaling proteins/phosphoproteins in cancer for 221 HER2-negative patients from 2 arms of the neoadjuvant I-SPY2 TRIAL (NCT01042379) for aggressive early stage breast cancer [119 Control; 102 Ganitumab].   This record also contains clinical data for these patients, including HR, and HER2 status, response (pCR or no pCR), and treatment arm. RPPA endpoints assayed are from hormone receptor (n=4), HER family (n=14), cell cycle/proliferation (n=20), immune (n=18), DNA repair deficiency (DDR; n=15), AKT/mTOR/PI3K (n=7), apoptosis/autophagy (n=10), IGF1R (n=6), TIE/ANG (n=4), growth/survival/metabolism (n=22) and RTK (n=19) and other pathways.  For gene expresson data for these patients, see the GEO record/subseries GSE194040.

overall_design: Reverse phase protein array (RPPA) array run on isolates from pre-treatment breast cancer biopsy samples that were first LCM-enriched for epithelial cells.    The sample characteristics and their values represent:    HER2: the status of the HER2 gene. 1 = positive; 0 = negative.    HR: the status of hormone (estrogen and progesterone) receptors.  1 = positive; 0 = negative.    pCR: the status of a pathological complete response (pCR).  1 = complete response; 0 = failed complete response    Arm: arm of the trial per patient, detailing treatment during taxol-phase of protocol:  Paclitaxil (Control arm: HER2- subset); Paclitaxel + Ganitumab.  All patients also received subsequent doxorubicin + cyclophosphamide.     Arm (short name): abbreviated name of treatment arm in the trial per patient (n=2 arms) - Control, Ganitumab                                                                  RPPA Array:  Platform Array version.  Key to convert from raw to normalized data.

first: Christina

last: Yau

first: Julia

last: Wulfkuhle

first: Emanuel

middle: F

last: Petricoin III

first: Douglas

last: Yee

first: Laura

last: van ‘t Veer


title: Biomarker genes for model-based prediction of drought-stress perception levels in rice

city: Tsukuba

first: Taiji

last: Kawakatsu

state: Ibaraki

address: 3-1-3 Kan-nondai

country: Japan

institute: National Agriculture and Food Research Organization

summary:
Background
Drought is a global challenge that severely restricts crop yields and threatens food security. Plants respond to drought stress by modulating gene expression before visible phenotypic changes occur. However, most studies of drought resistance have examined phenotypes after drought treatment, with little emphasis on how severely the plants were perceiving drought-stress conditions before the appearance of stress symptoms. We therefore developed drought-stress biomarkers (DSBMs) to detect drought-stress perception levels based on gene expression profiles by performing time-series transcriptome analysis and phenotypic analysis of rice (Oryza sativa) under drought conditions in the growth chamber.

Results
Time-series RNA-seq of the drought-susceptible rice cultivar IR64 revealed drastic changes in the transcriptome after 4–6 days of drought treatment in plants grown in pot culture mimicking drought conditions in the field, particularly for genes related to photosynthesis. Among the differentially expressed genes, we selected 23 DSBM genes that consistently responded to drought stress. Rehydration immediately reset the changes in expression of these DSBM genes, indicating that their expression changes reflect current drought-stress perception levels, but not stress memories. Responses of DSBM genes tended to be conserved among rice accessions, irrespective of the rice subpopulation (such as indica, aus, and japonica). We developed a machine learning model using the expression levels of DSBM genes trained by the time-series RNA-seq data for IR64. This model successfully predicted the drought-stress perception levels of various rice accessions, representing the probability of exposure to drought treatment, with an accuracy of 75%. Extreme root architecture traits, such as the largest root surface area, narrowest crown root diameter, and largest ratio of deep rooting, influenced the predicted drought-stress perception levels.

Conclusion
We identified DSBM genes and developed a machine learning model as a robust tool for assessing drought-stress perception levels in rice. Monitoring and predicting drought-stress perception levels should contribute to more efficient crop management and breeding schemes. Furthermore, our dataset would serve as a resource for further understanding the mechanisms of drought resistance in rice.

overall_design: RNA-seq profiling of IR64 rice leaves subjected to moderate and severe drought conditions for 0-12 days.

first: Kanami

last: Yoshino


overall_design: RNA-seq profiling of IR64 rice leaves subjected to severe drought conditions for 9 days, followed by irrigation for 6 days.


overall_design: RNA-seq profiling of WRC leaves at 5 days after moderate drought conditions


title: Single-cell analysis of human fibrous dysplasia bone reveals a fibrotic transcriptome and somatic, mosaic GNAS R201H/C mutations in endothelial, perivascular, and stromal cells

first: Edward

last: Hsiao

address: 505 Parnassus Ave

institute: UCSF

type: Genome variation profiling by high throughput sequencing

summary: Genetic mosaicism is a leading cause of human disease across the lifespan.  Improving the tools to detect somatic mosaicism and applying them to understand the cellular and molecular mechanisms that contribute to disease is of critical importance for improving human health.  Fibrous dysplasia (FD) is a prototypical disease of Gs-GPCR activation caused by somatic, mosaic GNAS R201H/C mutations that result in fibrotic bone.  Utilizing single-cell RNA sequencing and a unique GNAS genotyping strategy, we analyzed non-hematopoietic cells from FD and non-FD human bone. FD bone showed an altered fibroblast composition with a unique FD-specific osteoblastic cluster. Surprisingly, in addition to the skeletal stromal lineages, endothelial and perivascular cells also expressed GNAS R201H/C , which was confirmed using BaseScope, suggesting that GNAS R201H/C mutations are present in multiple non-osteogenic cell lineages.  We also identified a common fibrotic transcriptomic signature across FD cell lineages.  Our results highlight the effects of GNAS mosaicism on the cellular and transcriptomic landscapes of FD, identify previously unrecognized cell types that may be relevant to FD pathogenesis, and reframe our understanding of GNAS R201H/C function in bone.

overall_design: We performed single-cell RNA sequencing combined with single GNAS genotyping on non-hematopoietic cells from 4 (four)  fibrous dysplasia (FD) and 4 (four) non-FD human bone samples.

first: Kelly

last: Wentworth

first: Fernando

last: Fierro

first: Tania

last: Moody

first: Bryan

last: Le

first: Zachary

last: Michel

first: Alison

last: Boyce

first: Michael

last: Collins

first: Vardit

last: Kram

first: Luis

last: de Castro

first: Eric

last: Chow

first: Amir

last: Qorbani


title: cGAS-STING activation promotes innate and adaptive immunity crosstalk and enhances anti-tumor response

status: Public on Jul 25 2025

first: Zhichao

last: Ai

state: Shanghai

address: 371 Lishizhen Road

department: Oncology

institute: China Innovation Center of Roche (CICoR)

summary: The cancer-immunity cycle is regulated by a series of stimulatory and inhibitory factors. The Stimulator of Interferon Genes (STING) pathway, a key stimulator of type I interferon production, bridges innate and adaptive immunity to promote anti-tumor responses. Using a syngeneic pancreatic tumor model, we characterized the single-cell landscape changes induced by STING stimulation. Our findings revealed that STING agonist treatment reprograms transcription across multiple cell lineages, boosting innate immune responses and lymphocyte activation, thereby enhancing tumor killing. Single-cell transcriptome sequencing identified significant increases in monocytes, neutrophils, macrophages, and CD8 T cells, indicating augmented tumor inflammation. Differential gene expression analysis highlighted upregulated genes related to immune cell effector mechanisms and antigen presentation. Functional assays confirmed that STING activation enhances T cell-mediated tumor killing through myeloid cell activation. These results underscore the potential of STING agonists in reprogramming the tumor microenvironment to potentiate anti-tumor immunity, although clinical translation remains challenging due to pharmacokinetic limitations and potential systemic toxicity. Further research is needed to optimize STING agonist delivery and dosage for effective cancer immunotherapy.

overall_design: There are 4 mouse samples, consisting of tumour samples collected from tumour bearing mouse treated with vehicle or STING agonist EX-AC01, with whole tissue single cell sequencing.

first: Zhichao(Eric)


title: The impact of mab_1638 on the M. abscessus transcriptome

first: Scarlet

last: Shell

overall_design: The mab_1638 gene of M. abscessus strain ATCC19977 was disrupted with a transposon. Triplicate cultures of the parental and mab_1638::tn strains were grown to log phase and RNA harvested and used to contruct RNAseq expression libraries.

first: Daniel

last: Barkan

first: Michal

last: Bar-Oz

first: Junpei

last: Xiao

last: Meir

first: Manitosh

last: Pandey

first: Stefan

last: Oehlers


title: Nova-ST spatial transcriptomics of Lecanamab- and Lecanemab LALA-PG-treated xenotrasplanted human microglia [ST]

city: Leuven

first: Bart

last: de Strooper

address: Campus Gasthuisberg, Herestraat 49, bus 602

department: VIB-KU Leuven Center for Brain & Disease Research

country: Belgium

institute: KULeuven

summary: We investigated the effect of Lecanemab's Fc effector function on the transcriptomes of human microglia xenotransplanted in a mouse model of AD. We performed Nova-ST spatial transcriptomics analysis on xenografted mice treated with Lecanemab and Lecanemab LALA-PG, a human IgG1 variant designed to abolish Fc-mediated effector functions. We found that treatment with Lecanemab induced phagocytic and lysosomal reprogramming in the microglia surrounding plaques, an effect that was not present upon Lecanemab LALA-PG.

overall_design: Human embryonic stem cells (WiCell, #WA09) were differentiated into microglial precursors and grafted into AppNL-G-F Csf1rΔFIRE/ΔFIRE mice. At 4 months, the mice were chronically treated for 8 weeks with 10 mg kg−1 Lecanemab (n=2) or Lecanemab LALA-PG (n=2), dosed weekly intraperitoneally. One day after the final dose, mice were terminally anesthetized and Nova-ST spatial transcriptomics was performed on cryosections of the brains. Only the human (microglial) transcriptomes were analyzed.

first: Giulia

last: Albertini

first: Magdalena

last: Zielonka

first: Marie-Lynn

last: Cuypers

first: An

last: Snellinx

first: Ciana

last: Xu Ruchen

first: Suresh

last: Poovathinghal

first: Marta

last: Wojno

first: Kristofer

last: Davie

first: Veerle

last: van Lieshout

first: Katleen

last: Craessaerts

first: Leen

last: Wolfs

first: Emanuela

last: Pasciuto

first: Tom

last: Jaspers

first: Katrien

last: Horré

first: Lutgarde

last: Serneels

first: Mark

last: Fiers

first: Maarten

last: Dewilde

last: De Strooper


title: scRNA-seq of Lecanamab- and IgG1-treated xenotrasplanted human microglia

first: Bart

last: de Strooper

summary: We investigated the transcriptomic changes of human microglia xenotransplanted in a mouse model of AD upon treatment with Lecanamab (Lec) compared to control (IgG1). Single-cell RNA sequencing reveals that Lec treatment induces a transcriptional program in microglia that promotes amyloid plaque removal, involving pathways related to phagocytosis, metabolism, antigen presentation, unfolded protein response, and interferon response.

overall_design: Human embryonic stem cells (WiCell, #WA09) were differentiated into microglial precursors and grafted into AppNL-G-F and AppNL-G-F Csf1rΔFIRE/ΔFIRE mice. At 4 months, the mice were chronically treated for 8 weeks with 10 mg kg−1 Lecanemab or IgG1, dosed weekly intraperitoneally. One day after the final dose, mice were terminally anesthetized and human microglia were isolated for single-cell RNA-seq. Only the transcriptomes of the AppNL-G-F Csf1rΔFIRE/ΔFIRE mice were analyzed to evaluate the transcriptional response of human microglia cells to Lecanamab in this model.

first: Giulia

last: Albertini

last: Zielonka


title: Integrative assessment of RNA sequencing and in silico analysis to pinpoint mRNAs, lncRNAs, and circRNAs interactions with miRNAs underlying arsenic-induced neurotoxicity

status: Public on Jul 28 2025

city: Lucknow

first: Aditya

middle: Bhushan

last: Pant

state: Uttar Pradesh

address: vishvigyan Bhawan MG Marg

department: FEST

country: India

institute: CSIR-INDIAN INSTITUTE OF TOXICOLOGY RESEARCH

summary: The acquisition of neurodegeneration hallmarks necessitates molecular changes at multiple levels of functional genomics. Regulatory RNAs, including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs) play crucial roles in modulating messenger RNAs (mRNAs) expression and are potential molecules that regulate multifactorial neurotoxicity mechanisms. Integrated studies of regulatory RNAs’ functions are still lacking to portray the complete picture. In this study, we carried out a detailed analysis of mRNA, lncRNA, and circRNA profiles in differentiated SH-SY5Y cells exposed to arsenic, a well-known neurotoxicant, using the Illumina Novaseq6000 platform. Subsequently, employing a bioinformatics approach, we identified specific interactions between these RNA molecules and potential miRNAs, unraveling intricate regulatory networks. Among significantly deregulated transcripts, we identified 2487 mRNA transcripts, 1192 lncRNA transcripts, and 20 circRNA transcripts in arsenic-treated cells compared to control. Functional enrichment analysis indicated their involvement in numerous pathways underlying neurotoxicity. Further, these regulatory molecules displayed strong interactions with multiple miRNAs implicated in neuronal damage. Our findings revealed intricate molecular alterations in response to arsenic exposure, emphasizing the crucial role of multi-omics technologies in understanding neurodegeneration. These findings pave the way for targeted therapeutic interventions, focusing on precise modulation of regulatory RNA networks to mitigate the effects of arsenic.

overall_design: We have performed Illumina sequencing using the Novaseq6000 platform to identify differentially expressed microRNAs (mRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs) in differentiated SH-SY5Y cells in response to arsenic exposure.

first: AB

first: Sana

last: Sarkar

first: Anuj

last: Pandey

first: Bushra

last: Khan


title: Mutations in TAC1B drive increased CDR1 and MDR1 expression and azole resistance in Candida auris

city: Memphis

first: Katherine

last: Barker

address: 262 Danny Thomas Place, Mail Stop 313, Room I5200

department: Pharmacy & Pharmaceutical Sciences

institute: St. Jude Children's Research Hospital

summary: Objective: Candida auris has emerged as a fungal pathogen of particular concern owing in part to its propensity to exhibit antifungal resistance, especially to the commonly prescribed antifungal fluconazole. In this work we aimed to determine how mutations in the transcription factor gene TAC1B, which are common among resistant isolates and confer fluconazole resistance, exert this effect. Methods: Selected TAC1B mutations from clinical isolates were introduced into a susceptible isolate and reverted to the wild-type sequence in select clinical isolates using CRISPR Cas9 gene editing. Disruption mutants were likewise generated for select genes of interest. TAC1B mutants were subjected to transcriptional profiling by RNA-seq, and relative expression of specific genes of interest was determined by qRT-PCR. Antifungal susceptibilities were determined by modified CLSI broth microdilution. Results: TAC1B mutations leading to A640V, A657V, and F862_N866del conferred fluconazole resistance, as well as increased resistance to other triazoles, when introduced into a susceptible isolate. RNA-seq revealed that the ATP-Binding Cassette (ABC) transporter gene CDR1 as well as the Major Facilitator Superfamily (MFS) transporter gene MDR1 were both up-regulated by these TAC1B mutations. Disruption of CDR1 greatly abrogated resistance in strains with TAC1B mutations whereas disruption of MDR1 had little to no effect. However, disruption of both CDR1 and MDR1 resulted in an additional reduction in resistance as compared to disruption of either gene alone. Conclusion: TAC1B mutations leading to A640V, A657V, and F862_N866del all result in increased resistance to fluconazole and other triazole antifungals, and increased expression of both CDR1 and MDR1 in C. auris. CDR1 is the primary driver of resistance conferred by these TAC1B mutations.

overall_design: Strains were constructed by CRISPR-Cas9 gene editing from a Candida auris Clade Ic clinical isolate (Kw2999) in order to correct the endogenous ERG11 mutation and then modify the endogenous TAC1B gene to either the wildtype sequence or to harbor one of the following amino acid substitutions: A640V, A657V, or F682_N866del. Each of the strains examined in this study were grown to mid-log phase in YPD at 35degC. For RNA-seq expression analysis, strain 1c (ERG11-WT/TAC1B-WT) was used as the control comparator for each of the TAC1B mutant strains.

first: Darian

middle: J

last: Santana

first: Qing

last: Zhang

first: Tracy

last: Peters

first: Jeffrey

last: Rybak

first: Joachim

last: Morschhauser

first: Christina

last: Cuomo

first: David

last: Rogers


title: TRAP-seq in 3D Angiogenesis Assays Reveals Distinct Biological Processes Associated with Early and Late Morphogenesis that are Disrupted with PIK3CA-H1047R

city: Albany

first: Ramon

last: Bossardi Ramos

state: Ny

address: 43 New Scotland Avenue

department: Department of Molecular and Cellular Physiology

institute: Albany Medical College

summary: Endothelial cells (ECs) are often a minority cell type in a tissue, limiting the utility of bulk sequencing approaches.  Single cell sequencing lacks sensitivity and requires disruptive tissue digestion techniques.  TRAP seq (Translating Ribosome Affinity Purification) or “RiboTag” has been used to overcome these limitations. Co-culture systems allow primary ECs to differentiate and undergo tubular morphogenesis in cell culture, however similar limitations exist with these in vitro assays, as ECs are under-represented by as much as a factor of 10 in many assays.  We sought to use TRAP seq to better understand the gene expression landscapes that drive these morphogenic events. We found TRAP seq selectively enriches for endothelial RNA in both the planar and fibrin bead co-culture assays. Intriguingly, there are distinct changes in blood vessel development and in the mitotic cell cycle, unique to early and late phases of morphogenesis. To determine how these biological processes are altered by a known disruptor of vascular morphogenesis, we expressed PIK3CAH1047R in ECs, implicated as a driver in several types of vascular malformations. We found PIK3CAH1047R expression results in profound changes in endothelial cell expression with enrichment in genes associated with blood vessel morphogenesis gene ontology terms. There is a cohort of genes which showed dysregulation in both morphogenesis assays and these include numerous genes known to be important for tip/stalk specification during developmental angiogenesis, with a profound penetrance of NOTCH pathway dysregulation.

overall_design: HUVECs are infected with the pHAGE_Rpl22-3X-HA plasmid and seeded for either 2D culture or 3D planar co-culture. As biological variability is a factor when using primary cells, experiments were conducted using 4 independent pools of primary HUVECs from two different commercial vendors, each pool representing at least three donors of mixed races and sexes.  All cells from one lot are seeded simultaneously for all time points (day 1, day 4 or day 8). To ensure representative numbers of endothelial and fibroblast mRNAs in the 2D endothelial samples, identical numbers of endothelial and fibroblasts as used in 3D culture, were plated separately at the same time and media as the co-culture assays and were lysed in a common fraction of lysis buffer. Lysates were made from 2D and 3D cultures at day 1, and additional 3D cultures at day 4 and day 8 time points.

first: Samantha

last: King

first: Qing-fen

last: Li

first: Ian

last: Tschang

first: Ekta

last: Singh

first: Kevin

last: Pumiglia


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

status: Public on Jul 21 2025

city: New York

first: Ly-sha

last: Ee

address: 413 E 69th Street

institute: Weill Cornell Medicine

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

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

first: Matthias

last: Stadtfeld

first: Daniel

last: Medina-Cano

first: Alexander

last: Polyzos


title: A Human iPSC-derived Organoid System to Model Myelin Destruction and Repair

city: Parkville

last: Barton

address: Parkville Campus 30 Royal Parade

country: Australia

institute: The Florey

summary: We engineered a novel human iPSC-derived organoid system enriched with mature, myelinating oligodendrocytes and functionally reactive microglia. This model enables the study of human CNS remyelination following a demyelinating insult, encapsulating: myelin fragmentation, microglial clearance of myelin debris and oligodendrocyte genesis, differentiation, and axon ensheathment. This system provides a powerful and unparalleled capacity to interrogate complex human cell behaviour, relevant to those studying glial biology and neurological disease mechanisms.

overall_design: Dissociation of organoids into single cells for transcriptomic analysis was performed as per manufacturer’s protocol using a Papain Dissociation System (Worthington Biochemical). Briefly, 16 organoids per group were incubated in 20 U/mL papain enzyme solution at 37°C for 60 min. Every 15 min, gentle trituration was applied to each sample to break up cell clusters into a single cell suspension. After the digestion, DNase-protease inhibitor solution was added to single cell suspensions followed by centrifugation at 300 x g for 5 min. Cell pellets were then processed with the Chromium Gene Expression Flex Library Prep kit (10x Genomics) as per manufacturer’s protocol. Briefly, single cells were fixed overnight at 4 °C using 4 % PFA (ProSciTech) diluted in Concentrated Fix & Permealisation buffer (from Chromium Gene Expression Flex Library Prep kit). After fixation, cells were pelleted at 850 x g for 5 min. Cell pellets were quenched with Quenching and Enhancer buffer (from Chromium Gene Expression Flex Library Prep kit). Glycerol was added to each sample to a final concentration of 25 % prior to storing in -80 °C. Library preparation and sequencing were performed by AGRF sequencing facility (Australia). A single-cell suspension (~24,000 cells) was captured from all isolated cells per sample, without selection. Data was generated with the Illumina BCL Convert 4.1.5 pipeline.

first: Shwathy

last: Ramesan

first: Joel

last: Mason

first: Molly

last: EV Swanson

first: Samuel

last: A Mills

first: Sandeep

last: S Kumar

first: Heejung

last: Shim

first: Denis

last: Korneev

first: Georg

last: Ramm

first: Aaron

last: Andres

first: Lijun

last: Loh

first: Katherine

last: N Lewis

first: Francois-Xavier

last: E Beau

first: Stephanie

last: Chua

first: Miran

last: Mrkela

first: Bradley

last: Turner

first: Matthew

last: Rutar

last: G Gonsalvez

last: K Barton


title: Transcriptomic profiling of day 194 patient-specific pluripotent stem cell-derived alveolar epithelial type 2 cells expressing the SFTPCC121Y mutation and their gene-edited corrected counterparts

city: Boston

first: Pushpinder

last: Bawa

address: 670 Albany St

department: Boston University Medical Campus

institute: Center for Regenerative Medicine

summary: We performed transcriptomic profiling of cells derived from human induced pluripotent stem cells (iPSCs) using our previously described distal lung directed differentiation protocol to generate alveolar epithelial type 2 cells (iAT2s). We used the SPC8 human iPSC line and specifically the SPC8-ST-Corr (SFTPCtdT/WT) and SPC8-ST-Mut (SFTPCC121Y/tdT) clones containing a SFTPCtdTomato knock-in reporter. SFTPCtdTomato+ cells were sorted on days 45, 87 and 182 of differentiation. iAT2s were single-cell passaged in self-renewing 3D alveolosphere cultures approximately every 10-14 days through day 194. On day 194, all live cells were sorted and encapsulated for scRNA-seq using the 10X Chromium System. We find that a subset of mutant (SFTPCC121Y/tdT) iAT2s develops an aberrant transitional cell state.

overall_design: Global transcriptomic profiling of day 194 patient-specific induced pluripotent stem cell (iPSC)-derived alveolar epithelial type 2 cells (iAT2s) expressing the SFTPCC121Y mutation and their gene-edited corrected counterparts by scRNA-seq

first: Konstantinos-Dionysios

last: Alysandratos

first: Darrell

last: Kotton


title: The paradoxical significance of CD39+CD8+ T cells in clear cell renal cell carcinoma [scRNA-seq]

status: Public on Jul 23 2025

city: Daejeon

first: YEO

last: JINHEE

address: 291 Daehak-ro

country: South Korea

institute: Korea Advanced Institute of Science and Technology

summary: CD39+CD8+ T cells are known as tumour antigen-specific cells among CD8+ tumour-infiltrating lymphocytes (TILs). However, CD39+CD8+ T cells also reportedly exhibit immunosuppressive activity in hypoxic tumour models. Here we investigated CD39+CD8+ TILs with regards to their molecular phenotypes, developmental mechanisms, functions, and prognostic significance in clear cell renal cell carcinoma (ccRCC), a VHL mutation-associated hypoxic tumour. Single-cell RNA and TCR analyses confirmed that CD39+CD8+ cells are a terminally exhausted subset of tumour-specific CD8+ TILs. CD39+CD8+ T-cell development was highly correlated with cAMP signals, and was directly induced by cAMP and TCR signallings. Analysis of an RCC cohort revealed a markedly elevated proportion of CD39+ cells among CD8+ TILs in ccRCC, compared to non-ccRCC. Moreover, the proportion of CD39+CD8+ TILs was associated with high tumour mutational burden and hypoxic features. Ex vivo functional assays revealed that CD39+CD8+ TILs exerted immunosuppressive activity on neighbouring CD8+ T cells via ectonucleotidase activity- and adenosine-dependent mechanisms. CD39+CD8+ TIL enrichment predicted poor prognosis of ccRCC patients, yet also predicted favourable treatment responses to anti-PD-1 therapy. This paradoxical prognostic significance in ccRCC is explained by the dual properties of CD39+CD8+ TILs: tumour antigen specificity and immunosuppressive activity.

overall_design: From single-cell suspensions of tumours and PBMCs, CCR7-CD45RA- and CCR7-CD45RA+ CD8+ T cells were sorted. Next, these cells were loaded onto the 10× Genomics Chromium Single Cell platform.

first: Eui-Cheol

last: Shin

first: Yong Joon

last: Lee

first: Seung Hyuck

last: Jeon

first: Jin Hee

last: Yeo

first: Sun-ju

last: Byeon


title: Serotonin 2A Receptor Attenuates Psoriatic Inflammation by Suppressing IL-23 Secretion in Monocyte-derived Langerhans cells (mouse)

city: Taipei City

first: Yeh Fong

last: Tan

state: Taipei

address: No. 128, Section 2, Academia Rd, Nangang District

department: Institute of BioMedical Sciences

country: Taiwan

institute: Academia Sinica

summary: Serotonin and its receptor are known to play a role in regulating immune cells. However, how they affect an autoimmune disease like psoriasis is not well-established and the mechanism remains to be elucidated. Here, we investigated the role played by serotonin 2A receptor (HTR2A) in regulating psoriasis. HTR2A antagonistic drug worsens psoriatic outcome and HTR2A modulation reduced psoriatic inflammation. Using Imiquimod-induced psoriasiform inflammation model, HTR2A-deficient mice experienced exacerbated inflammation. Hematopoietic cells, particularly monocyte-derived Langerhans cells, were responsible for this exacerbated inflammation. Mechanistically, the exacerbated inflammation is due to increased interleukin-23 (IL-23) secretion and HTR2A suppresses it by inhibiting the activation of non-canonical NFkB pathway. Platelet-derived serotonin is the putative agonist modulating HTR2A attenuating psoriatic inflammation. Lastly, our findings in mice were also reproduced clinically. Thus, our data demonstrate platelet serotonin putatively modulates HTR2A attenuating psoriatic inflammation by suppressing IL-23 secretion via inhibiting non-canonical NFkB pathway in monocyte-derived Langerhans cells.

overall_design: Transcriptomic analysis of RNA-seq data of isolated HTR2A deficient Langerhans cells treated with Imiquimod and a-CD40L.

first: Yeh

first: Chen-Yun

last: Yeh

first: Ching-Hui

last: Tsai

first: Yungling


title: Aberrant Transitional Alveolar Epithelial Cells Promote Pathogenic Activation of Lung Fibroblasts in Preclinical Fibrosis Modeling (scRNAseq)

city: Philadelphia

first: Jeremy

last: Katzen

state: PA

address: 3450 Hamilton Walk, Stemmler Hall 216

institute: University of Pennsylvania Perelman School of Medicine

summary: CD44+ and CD44- negative Alveolar type 2 cells (AT2) represent distinct populations in lung fibrosis. To charecterize these cells, we isolated CD44+/- AT2s from WT mice and from fibrotic Sftpc muant lungs and performd RNA sequencing no these populations

overall_design: To enrich for EPCAM+ cells and mesenchymal cells , a single cell suspension was prepared by physical and enzymatic dissociation (Collagenase, DNase, Dispase) from Sftpc mutation firbosis lungs (n=2) and control lungs (n=2) followed by MACS sorting by LS columns with CD45+ and CD31 cell removal using CD45 and CD31 micobeads followed by EPCAM+ cell enrichment using EPCAM microbeads. CD45-/CD31-/EPCAM- cells were considered lung mesenchymal cells. EPCAM+ and mesenchymal cells were prepared in 50/50 concentration for sequencing.

first: Evan

middle: T

last: Hoffman

first: Willy

last: Roque Barboza

first: Luis

last: Rodriguez

first: Rachna

last: Dherwani

first: Kasey

last: Minakin

first: Yaniv

last: Tomer

first: Dakota

last: Jones

first: Aditi

last: Murthy

first: Adam

last: Bennett

first: Ana

last: Nottingham

first: Feiya

last: Wang

first: Apoorva

last: Babu

first: Katrina

last: Chavez

first: Charlotte

last: Cooper

first: Maria

last: Basil

first: Micha

last: Brickman Raredon


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

status: Public on Jul 22 2025

city: Princeton

first: Celeste

last: Nelson

address: 25 William St

institute: Princeton University

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

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

first: Maryam

last: Kohram

first: Carolina

last: Trenado-Yuste

first: Molly

last: Brennan-Smith

first: Evelyn

last: Navarro Salazar

first: Pengfei

last: Zhang

first: Jasmine

last: Hao

first: Xincheng

last: Xu

first: Bharvi

last: Chavre

first: William

last: Oh

first: Sherry

middle: X

first: Susan

last: Leggett

first: Rolf-Peter

last: Ryseck

first: Joshua

middle: D

last: Rabinowitz


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

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

institute: MRC London Institute of Medical Sciences

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

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

first: Andrew

last: Dimond

first: Do

last: Gim

first: Elizabeth

last: Ing-Simmons

first: Chad

last: Whilding

first: Holger

last: Kramer

first: Dounia

last: Djeghloul

first: Alex

last: Montoya

first: Bhavik

last: Patel

last: Cheriyamkunnel

first: Karen

last: Brown

first: Pavel

last: Shliaha

first: Juan

last: Vaquerizas

first: Matthias

last: Merkenschlager

first: Amanda

middle: G

last: Fisher


title: Serotonin 2A Receptor Attenuates Psoriatic Inflammation by Suppressing IL-23 Secretion in Monocyte-derived Langerhans cells

first: Yeh Fong

last: Tan

overall_design: Transcriptomic analysis of RNA-seq data of human skin treated with 2,5-Dimethoxy-4-iodoamphetamine (DOI) or Phosphate Buffered Saline.

first: Yeh

first: Chen-Yun

last: Yeh

first: Ching-Hui

last: Tsai

first: Yungling

middle: L

last: Lee


title: Genetic variation in the activity of a TREM2-p53 signaling axis determines oxygeninduced lung injury

status: Public on Jul 24 2025

city: La Jolla

first: Christopher

last: Benner

state: California

address: 9500 Gilman Dr. MC 0640

department: Medicine

institute: University of California, San Diego (UCSD)

summary:
To investigate the role of Trem2 in neonatal hyperoxia induced lung injury, we exposed mice to 75% oxygen for 14 days.
We then performed gene expression profiling in whole lung and bone marrow derived macrophages using RNA-seq. We studied gene regulation using ChIP-seq.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for lungs exposed to hyperoxia and room air controls. ChIP-seq analysis to assess p53 binding in the lung and macrophages after hyperoxia exposure.

first: Yohei

last: Abe

first: Nathanael

last: Spann

first: Wenxi

last: Tang

first: Robert

last: Huff

first: Sean

last: Jansky

first: Richard

last: John

first: Kelly

last: Chanthavixay

first: Debanjan

last: Dhar

first: Souradipta

last: Ganguly

first: Cadence

last: Seymour

first: Miguel

last: Mooney

first: Jason

last: Guo

first: David

last: Lopez

first: Michael

last: Longaker

middle: K

last: Glass

first: Eniko

last: Sajti


title: Prolonged Glucagon Exposure Rewires Lipid Oxidation and Drives Diabetic Kidney Disease Progression

status: Public on Jul 18 2025

city: Beijing

first: Jingwen

last: Chen

address: 1 XianNongTan Street, Xicheng District

institute: Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical （CAMS & PUMC）

summary: Diabetic kidney disease (DKD) is the leading cause of end-stage kidney disease (ESKD), and few treatment options are available today to prevent the progressive loss of renal function. Tubular abnormalities may precede glomerular pathology early and indicate the functional progression of DKD, however, pathological mechanisms that initiate tubular abnormalities are poorly understood. Here, we found that glucagon receptor (Gcgr) is specifically and highly expressed in proximal tubular cells (PTEC) of kidney. Glucagon injection exacerbated lipid accumulation, glycogen content, inflammation, fibrosis, and renal injury, along with morphology changes on proximal tubules, podocytes, glomerular basement membrane (GBM), and mitochondria in the early phase of DKD mice. Whereas, the specific knockdown or knockout of Gcgr in PTEC of kidney almost completely halted the development of DKD. In contrary to the effect of short-term glucagon stimulation on fatty acid oxidation, long-term glucagon exposure led to glucagon reversal in PTEC, which is characterized by reduced energy production and promoted lipogenesis, and this effect was through the Gcgr-PKA-Creb-mTOR pathway. Accordingly, anti-GCGR antibody treatment greatly blocked the pathogenesis of DKD induced by both type 2 and type 1 diabetes. Thus, our results revealed a novel role of glucagon/GCGR signaling in PTEC lipogenesis and DKD, and Gcgr would be a promising therapeutic drug target for the treatment of DKD.

overall_design: To investigate the lipogenesis function of glucagon in kidney PTEC, we established  Gcgr PTEC specific knockdown mice by shRNA.We then performed gene expression profilling analysis using data obtained from RNA-seq of 3 different groups of mice kidney.Comparative gene expression profilling analysis of RNA-seq data for control, Ctr shRNA and Gcgr shRNA group.

first: Pingping

last: Li

first: Xingfeng

last: Liu


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

first: Ly-sha

last: Ee

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

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

first: Matthias

last: Stadtfeld

first: Daniel

last: Medina-Cano


title: An improved nuclei isolation protocol from leaf tissue for single-cell transcriptomics

status: Public on Jul 17 2025

city: Gainesville

last: Balmant

state: FL

address: 1253 Fifield Hall, Room 2204

department: Horticultural Sciences

institute: University of Florida

summary: We developed an alternative method for isolating nuclei to be utilized in scRNA-seq experiments from Zea mays leaves with reduced chloroplast contamination. By effectively removing chloroplasts during the FACS step of our protocol, using the autofluorescence from the chloroplasts, we achieved improved alignment of reads to the genome and transcriptome. Our enhanced protocol offers a valuable solution for applying snRNA-seq in tissues with a high content of chloroplasts.

overall_design: After nuclei isolation following Conde et al (2021), we used a FACS strategy for clean-up and enrichment of the nuclei using a BD FACSAriaTM IIU/III upgraded cell sorter. We used a double-filter strategy to negatively select autofluorescent chloroplast and positively select DAPI-stained nuclei (Fig 1). The Peridinin-Chlorophyll-Protein (PerCP) filter, excited by the 488 nm blue laser and captured with a 670/30 nm bandpass filter, was used to remove the events that emitted in this range. After this, the DAPI-positive population was selected according to emission in the 450/50 nm bandpass filter and then based on size and granularity using the forward versus side scatter (FSC vs SSC) plot. Finally, the selected population corresponding to nuclei was sorted, aiming for 40,000 nuclei for library preparation using 10X Genomics sc-RNAseq kit.


title: Paired-Tag single-cell joint profiling of H3K27me3-H3K4me1 and transcriptome revealed prenatal e-cigarette induced abnormal neuronal lineage development in rat neonatal prefrontal cortex

city: Loma Linda

first: Charles

last: Wang

state: CA

address: 11021 Campus Street

department: Department of Basic Sciences

institute: Loma Linda University

summary: We performed single-nucleus joint profiling of transcriptome and histone modifications, namely H3K27me3 and H3K4me1, in prenatal electronic cigarette exposed neonatal rat prefrontal cortex. We found that e-cig not only induced unique histone mark patterns for H3K27me3-H3K4me1 within the gene body in many cell type-specific marker genes, e.g., Fibcd1, Slc1a3, Apq4, and Rfx4, but also caused a differential gene expression for these genes. We demonstrated that H3K27me3-H3K4me1 bivalency regulated the neuronal lineage differentiation by controlling the accessibility of promoter regions in genes  responsible for cell specifications. Prenatal e-cig exposure also caused differential gene expressions in both excitatory and inhibitory neurons in many genes involved in specific neuronal functions, which was orchestrated by different H3K27me3-H3K4me1 methylations. Furthermore, prenatal e-cig smoking altered the gene expression of circadian genes involved in circadian entrainment and circadian rhythm including calcium signaling genes Cacna1c, Camk2b, and Ryr2; cAMP and protein kinase signaling transduction gene Adcy1 and Prkcb; as well as synaptic transmitter receptor Gria4. These results suggested that nicotine addiction could be epigenetically imprinted at a very early stage of brain development. Our study showed a profound effect of epigenomic regulation of histone marks by prenatal e-cig exposure on neuronal lineage development and highlighted a new underlying epigenetic mechanism of nicotine addiction, which could potentially lead to the identification of therapeutical targets for nicotine abuse disorders.

overall_design: Pregnant rats were exposed to e-cigarette vapor during E4 to E20. Paired-Tag single-cell joint profilling were performed on transciptome and H3K27me3-H3K4me3 in postnatal day 7 ( P7) brain prefront cortex to study the epigenetic influence of maternal vaping on rat neonates' brain development.


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

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

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