title: Pharmaco-behavioral Profiling Identifies Suppressors of Autism Gene-Associated Phenotypes in Zebrafish

city: New Haven

first: Priyanka

last: Jamadagni

state: CT

address: 333 Cedar Street

department: School of Medicine

institute: Yale University

summary: In this study, we establish a pharmaco-behavioral database of behavioral signatures of 520 U.S. FDA-approved drugs using high-throughput assays of basic sensory processing and arousal behaviors in larval zebrafish and define highly conserved effects of common psychotropic medication targets. By leveraging the behavioral profiles of nine large-effect ASD gene mutants, we identify enrichment of pharmacological mechanisms that anti-correlate with subgroups of ASD genes informed by a precision medicine approach.

sample_organism:
Danio rerio
Homo sapiens

platform_organism:
Danio rerio
Homo sapiens

overall_design: A comparative gene expression profile of zebrafish brains and hPSC derived iGluts with mutations for two autism risk genes - dyrk1a and scn1lab (zebrafish); SCN2A and DYRK1a (hPSCs) - after treatment with Levocarnitine.

first: Yi

last: Dai

first: Yunqing

last: Liu

first: Hellen

last: Weinschutz Mendes

first: April

last: Pruitt

first: Suha

last: Khan

first: Liang

last: Yang

first: Tzu-Chieh

first: Xiayuan

first: P.J. Michael

last: Deans

first: Novin

last: Balafkan

first: Dejian

last: Zhao

first: Gang

last: Xu

first: Yihan

first: Ningshan

last: Li

first: Weimiao

last: Wu

first: Sarah E.

last: Fitzpatrick

first: Uma

last: Neelakantan

first: Tianying

last: Chen

first: Christina

last: Szialta

first: David S.

last: Jin

first: Cheryl M.

last: Lacadie

first: Sheila

last: Umlauf

first: Xenophon

last: Papademetris

first: Yulia V.

last: Surovtseva

first: Kristen

last: Brennand

first: Zouheng

first: Ellen J.

last: Hoffman


title: Oncogenic and tumor-suppressive forces converge on a progenitor-orchestrated niche to shape early tumorigenesis [Xenium]

status: Public on Mar 18 2026

city: New York

first: Yu-Jui

last: Ho

state: New York

address: 417 E 68th St

department: Cancer Biology & Genetics Program

country: USA

institute: Memorial Sloan Kettering Cancer Center

summary: The transition from benign to malignant growth is a pivotal yet poorly understood step in cancer progression that marks the shift from a pathologically inert condition to a clinically lethal disease. Here, we integrate lineage tracing, single-cell and spatial transcriptomics to visualize the molecular, cellular and tissue-level events that promote or restrain malignancy during the tumor initiation in mouse models of pancreatic ductal adenocarcinoma (PDAC). We identify a discrete progenitor-like population of KRAS-mutant cells that co-activates oncogenic and tumor-suppressive programs—including p53, CDKN2A, and SMAD4—engaging senescence-like responses and remodeling their microenvironment, ultimately assembling a niche that mirrors invasive PDAC. Even brief KRAS inhibition in the epithelial compartment depletes progenitor-like cells and dismantles their niche, substantially delaying cancer initiation. Conversely, p53 suppression enables progenitor cell expansion, epithelial–mesenchymal reprogramming, and immune-privileged niche formation. These findings position the progenitor-like state as the convergence point of cancer-driving mutations, plasticity, and tissue remodeling—revealing a critical window for intercepting malignancy at its origin.

overall_design: Spatial transcriptomic using Xenium (10X) of mouse premalignant pancreas. All samples come from mice with oncogenic KrasG12D activation in pancreatic epithelial cells during embryonic development (Ptf1a-Cre; LSL-KrasG12D). Each sample metadata specifies the experimental condition:   1. K2_ctrl: p53 proficient pancreatic epithelium, subjected to injury-induced pancreatitis on day -1 and day 0, sample collected on day 2.  2. K2d1_ctrl: p53 proficient pancreatic epithelium, subjected to injury-induced pancreatitis on day -1 and day 0, sample collected on day 2.  3. K3_ctrl: p53 proficient pancreatic epithelium, subjected to injury-induced pancreatitis on day -1 and day 0, sample collected 3 weeks after.  4. K2_shp53: p53 knockdown in pancreatic epithelium, subjected to injury-induced pancreatitis on day -1 and day 0, sample collected on day 2.  5. K2d1_shp53: p53 knockdown in pancreatic epithelium, subjected to injury-induced pancreatitis on day -1 and day 0, sample collected on day 2.  6. K3_shp53: p53 knockdown in pancreatic epithelium, subjected to injury-induced pancreatitis on day -1 and day 0, sample collected 3 weeks after.  7. K2_MRTX1133: p53 proficient pancreatic epithelium, subjected to injury-induced pancreatitis on day -1 and day 0, followed by 5 doses of MRTX1133 (two doses per day). Sample collected after the fifth dose.  8. K2_vehicle: p53 proficient pancreatic epithelium, subjected to injury-induced pancreatitis on day -1 and day 0, followed by 5 doses of vehicle (two doses per day). Sample collected after the fifth dose.  9. K4: p53 proficient pancreatic epithelium without injury. Collected 4.5 months after birth.

first: José

last: Reyes

first: Scott

middle: W

last: Lowe

first: Dana

last: Pe'er


title: The Molecular Brake: Piezo1 Activation Delays Epithelial Gap Closure Through Transcriptional Downregulation of Adhesion Machinery

city: Amherst

first: Han

last: Jiang

state: MA

address: 240 Thatcher Rd, N572 SUN Lab, LIFE SCIENCE LAB

department: Mechanical Engineering

institute: University of Massachusetts Amherst

type: Expression profiling by high throughput sequencing

summary: The mechanosensitive ion channel Piezo1 is a critical regulator of epithelial homeostasis, influencing processes such as proliferation, extrusion, and wound healing. However, its role is highly context-dependent, with studies reporting both pro-migratory and inhibitory effects on gap closure. Here, we investigate the specific role of Piezo1 activation in a model of large epithelial gap closure using Madin-Darby Canine Kidney (MDCK) cells. We demonstrate that pharmacological activation of Piezo1 with Yoda1 significantly delays the closure of large gaps in a confluent monolayer. This delayed closure is not driven by changes in cell proliferation, pointing instead to a direct effect on the mechanics of collective cell migration. To elucidate the underlying molecular mechanism, we performed bulk RNA-sequencing on Yoda1-treated versus control MDCK cells. Transcriptomic analysis revealed that Piezo1 activation leads to significant differential expression of genes associated with integrin signaling, extracellular matrix (ECM) organization, and focal adhesions (FAs). These findings suggest that Yoda1-mediated Piezo1 activation impedes epithelial gap closure by modulating the transcriptional programs that govern cell-matrix adhesion and cytoskeletal dynamics, thereby disrupting the collective migration required to heal a large wound. This study provides new insights into the context-dependent inhibitory role of Piezo1 in epithelial repair and highlights the transcriptional axis through which it may operate.

overall_design: Bulk RNA-seq profiling of differential gene expression in MDCK cells treated with Yoda1 for 12 hr and 24 hr.

first: Ravi

last: Ranjan

first: Yubing

last: Sun


title: Developmental gene expression patterns driving species-specific cortical features

city: Geneva

first: Awais

last: Javed

address: Chemin des mines, 9

department: Fundamental Neurosciences

country: Switzerland

institute: University of Geneva

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The cerebral cortex shows species-specific variations in size and organization, likely accounting for distinct behavioral abilities. These structural differences may reflect evolutionary changes in the developmental expression of shared genes. To investigate this possibility, we used machine vision to identify and compare cell-type-specific gene expression patterns in the developing mouse and human neocortex, and in human cortical organoids. This identified genes with evolutionary conserved/divergent transcriptional regulation, revealing species-specific cyto-temporal gene expression patterns. Among such genes, the transcription factor JUNB showed mutually exclusive expression in human progenitors and mouse neurons. Through cell-type-specific gain- and loss-of-function experiments in mice and human organoids, we show that JUNB bidirectionally controls human cortical features, including progenitor proliferation rates, neuronal production timing, and total neuronal output. We identify IRF1 as a human RG-specific regulator that, when expressed in mouse RG, activates JUNB and recruits human-like gene regulatory networks, demonstrating cross-species activation of poised developmental programs. Together, these findings reveal how cyto-temporal regulation of shared genes drives species-specific cortical features and provides a molecular framework to understand and manipulate these evolutionary programs.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Single nucleus/cell RNA sequencing with or without TrackerSeq barcoding was performed on embryonic mouse cortex electroporated samples with control, hJUNB, hIRF1, hEGR1. CUT&RUN/Tag assays were performed on embryonic mouse cortex electroporated samples with control or hJUNB overexpression and iPSC-derived human cortical organoids.

first: Lucia

last: Gomez

first: Veronica

last: Pravata

first: Moein

last: Sarhadi

first: Quentin

last: Lo Giudice

first: Timea

last: Szalai

first: Lea

last: Aubert

first: Theo

last: Ribierre

first: Laurent

last: Nguyen

first: Silvia

last: Capello

first: Denis

last: Jabaudon

first: Esther

last: Klingler


title: Light and excessive CO2 uptake inhibit growth of Synechococcus sp. PCC 7002 under very high CO2 levels

city: Helsingør

first: Niels-Ulrik

last: Frigaard

address: Strandpromenaden 5

department: Department of Biology

country: Denmark

institute: University of Copenhagen

summary: Cultivation of photosynthetic microbes under elevated CO2 is widely used in biotechnology to enhance growth. However, very high CO2 levels inhibit growth for reasons that are not always clear. We established a method that allowed cultivation under different CO2 concentrations and controlled pH to study the cyanobacterium Synechococcus sp. PCC 7002. Growth rates, cell composition, and transcriptomic profiles were investigated under limiting (0.04%), optimal (1-4%), and inhibitory high (15-30%) gas phase CO2 contents, while maintaining pH approx. 7.5. At intermediate light (200 µmol /m2 /s), the growth rate at 30% CO2 was approx. 45% of that under optimal conditions. Under low light (<100 µmol /m2 /s), growth was less inhibited by high CO2 than at higher light intensities. Pigmentation and photosynthesis likewise decreased under high CO2, except that carotenoids indicative of high-light stress increased. Transcriptome sequencing confirmed that the photosynthesis machinery was downregulated and stress responses were upregulated under high CO2. Genetic knockdown of CO2 uptake (ndhF3 and ndhF4) or overexpression of a heterologous Na+/H+ antiporter (nhaS3) improved tolerance to high CO2, while knockdown of the CcmR transcriptional regulator reduced it. We conclude that the inhibiting species under very high inorganic carbon conditions was CO2, and not HCO3-, and that reduced light intensity or genetically suppressing active CO2 uptake improved the tolerance of Synechococcus to very high CO2 conditions. This work provides a basis for cultivation under a very wide range of CO2 concentrations, thereby broadening the scope for metabolic manipulation and biotechnological applications of cyanobacteria. (Algal Research)

overall_design: We performed targeted genetic manipulation (CRISPR interference knockdown of CO2 uptake (ndhF3 and ndhF4) and overexpression of a heterologous Na+/H+ antiporter (nhaS3)) in Synechococcus sp. PCC 7002. Transcriptome sequencing was performed to understand the mechanisms of CO2 toxicity and improve cellular tolerance to very high CO2 concentrations.

first: Carrasquer-Alvarez

last: Elena

first: Sven Geissler

last: Adrian

first: Abraham

last: Joshua Papa

first: Gorodkin

last: Jan

first: Pfleger

last: Brian Frederick

first: Seemann

last: Stefan Ernst

first: Frigaard

last: Niels-Ulrik


title: Transcriptomic profiling of pancreatic stellate cells and pancreatic cancer cells in a gemcitabine-driven tumor-stroma supernatant transfer model

city: Marburg

first: Mark

last: Schmitt

address: Karl-von-Frisch-Str. 2

country: Germany

institute: Institute of Pharmacology, University of Marburg

summary: Pancreatic ductal adenocarcinoma (PDAC) is characterized by extensive tumor-stroma interactions that influence disease progression and therapy response. To investigate transcriptional changes associated with chemotherapy-induced tumor-stroma signaling, RNA sequencing was performed in a supernatant transfer system. Murine pancreatic cancer cells (KPC4) were treated with gemcitabine, and supernatants from gemcitabine-treated or vehicle-treated tumor cells were transferred to murine pancreatic stellate cells (PSC4). In a second experiment, supernatants from PSC4 cells previously exposed to tumor cell supernatants were transferred back to pancreatic cancer cells. RNA sequencing was performed to characterize gene expression changes associated with chemotherapy-induced tumor-stroma communication.

overall_design: Murine pancreatic stellate cells (PSC4) were treated with supernatants derived from vehicle-treated (Control-SU) or gemcitabine-treated (Gem-SU) murine pancreatic cancer cells (KPC4). RNA sequencing was performed to analyze transcriptional changes induced in PSC4 cells by tumor cell-derived supernatants. In a second experiment, murine pancreatic cancer cells (KPC4) were treated with supernatants derived from PSC4 cells previously exposed to Control-SU or Gem-SU (Control-PSC-SU and Gem-PSC-SU). RNA sequencing was performed to analyze transcriptional responses of tumor cells to therapy-educated stromal cells. Three biological replicates were analyzed for each condition.

first: Ciarán

last: McDonnell

first: Valeriya

last: Zinina

first: Amina

last: Othman

first: Larissa

last: Launhardt

first: Anna

last: Brichkina

first: Fatma

last: Aktuna

first: Magdalena

last: Brkic

first: Matthias

last: Lauth

first: Eliana

last: Stanganello


title: Transcriptomic analysis of Primary B-cell target genes upon infection with Epstein-Barr Virus (EBV) expressing wildtype (WT) or mutant  Latent Membrane Protein 1 (LMP1)

city: Boston

first: Bidisha

last: Mitra

address: 181 Longwood Avenue, 8th floor

department: Medicine

institute: Brigham and Women's Hospital

summary: RNA-seq was used  to characterize the LMP1 mediated regulation of host B-cell gene regulation. We infected Primary B-cells with Bacterial Artificial Chromosome (BAC)-derived WT LMP1 or TES1 mutant or TES2 mutant or TES1/TES2 double mutant LMP1 expressing EBV. Samples were assessed for transcriptomics effect on the host B-cell landscape at D7 post-infection and D21 post-infection.Because the TES1m and DM infected B-cells donot survive past D21 post-infection, D21 samples included WT vs TES2minfected B-cells only.

overall_design: Comparative gene expression profiling analysis of RNA-seq data in Primary B-cells upon infection with EBV expressing WT or  transformation effector site(TES) domain single or double mutant. Samples were collected for Bulk RNA-seq at D7 post-infection and Day 21 post-infection (Only for the WT and TES2m)

first: Nina

last: Beri

first: Makoto

last: Ohashi

first: Eric

last: Burton

first: Benjamin

middle: E

last: Gewurz


title: Oncogenic and tumor-suppressive forces converge on a progenitor-orchestrated niche to shape early tumorigenesis [injury_shp53_scRNA-seq]

first: Yu-Jui

last: Ho

overall_design: To assess the spectrum and dynamics of premalignant states and tissue remodeling events in the in the context of oncogenic KRAS activation in the premalignant epithelium, we subjected 5–6-week-old male mice with eight-hourly intraperitoneal injections of 80 μg kg-1 of caerulein (Bachem) for two consecutive days (16 injections total). Caerulein dose was adjusted to body weight at the beginning of each day of treatment. We harvested the pancreata at 3 weeks post-caerulein treatment, collecting single cells for scRNA-seq.

first: José

last: Reyes

first: Scott

last: Lowe

first: Dana

last: Pe'er


title: Oncogenic and tumor-suppressive forces converge on a progenitor-orchestrated niche to shape early tumorigenesis [FLEX]


title: m6Am methyltransferase PCIF1 regulates osteogenesis via WNT signaling

city: Chengdu

first: Quan

last: Yuan

address: No.14, 3Rd Section of Ren Min Nan Road, Sichuan

country: China

institute: West China Hospital of Stomatology, Sichuan University

summary: Mesenchymal stem cells (MSCs) were isolated from Prrx1-Cre;Pcif1fl/fl mice and Pcif1fl/fl littermates and cultured in osteogenic medium for 7 days to investigate the role of Pcif1 in osteogenic differentiation. Total RNA was extracted using Trizol reagent and purified with poly-T oligo-attached magnetic beads. Sequencing libraries were prepared and sequenced on an Illumina PE150 platform. Raw reads were processed and mapped to the Mus musculus reference genome (mm10) using HISAT2. Differential gene expression analysis was performed with the DESeq2 R package using thresholds of |fold change| ≥ 2 and adjusted p-value ≤ 0.05. Gene Ontology (GO) and KEGG pathway enrichment analyses were conducted using the clusterProfiler R package to identify biological processes and pathways affected by Pcif1 deletion during osteogenic differentiation. This dataset provides insights into the transcriptional programs regulated by Pcif1 in MSC osteogenesis.

overall_design: Gene expression profiling of MSCs from Prrx1-Cre;Pcif1fl/fl and Pcif1fl/fl mice during osteogenic differentiation. Samples were collected in biological duplicates after 7 days of culture in osteogenic medium. RNA-seq libraries were prepared and sequenced using Illumina PE150.

first: Wei

last: Song

first: Qi

last: Yin


title: Effects of liraglutide on skeletal muscle transcriptome in diet-induced obese C57BL/6 mice

city: Taiyuan

first: Huan

last: Xue

state: Shanxi

address: No. 56 Xinjian South Road

institute: Shanxi Medical University

summary: Metabolic diseases have become a major global health burden. Insulin resistance plays a critical role in the development and progression of metabolism‑related disorders. Glucagon‑like peptide‑1 receptor agonists (GLP‑1RAs) have emerged as groundbreaking therapeutic agents for the management of a wide spectrum of metabolic diseases. As skeletal muscle is the primary site of insulin‑stimulated glucose disposal, and muscle insulin resistance is a central feature of abnormal glucose metabolism in obesity. To investigate the effects of GLP‑1RAs on the transcriptomic profile of skeletal muscle, we administered liraglutide to diet‑induced obese (DIO) mice and collected skeletal muscle tissues for transcriptome sequencing.

overall_design: Twenty-four-week-old C57BL/6 DIO mice were divided into the model group (n=8) and liraglutide group (n=8). Mice in the liraglutide group received subcutaneous injections of Liraglutide (0.2 mg/kg/day) for 9 weeks, while mice in the  model groups were administered normal saline. Four skeletal muscle tissue samples per group were collected for transcriptome sequencing.

first: Yi

last: Zhang

first: Yun

middle: F

last: Liu

first: Zhi

middle: H

last: Lu


title: Inhibition of BIRC5 and MCL-1 as a potential treatment strategy to overcome drug resistance in Mantle Cell Lymphoma

city: AUBURN

first: Amit

middle: Kumar

state: AL

address: HARRISON COLLEGE OF PHARMACY

department: DRUG DISCOVERY AND DEVELOPMENT

institute: AUBURN UNIVERSITY

summary: Mantle cell lymphoma (MCL) is a difficult-to-cure, highly heterogeneous, and aggressive form of non-Hodgkin lymphoma with a high recurrence rate and poor long-term prognosis. Using a novel optimization-regularization-based computational prediction algorithm called "secDrug," we have identified therapeutic targets for treating resistant cancers. When applied to B-cell malignancies, the secDrug algorithm predicted the pro-survival proteins BIRC5 and MCL1 as top targets. Here, using a panel of MCL cell lines representing PI/BTKi sensitive, innate resistance, and clonally derived acquired resistance, we demonstrated that small molecule-based inhibition of BIRC5 and MCL1 is effective in killing MCL cells as single agents and in combination with Bortezomib or Ibrutinib. Further, using RNAseq (transcriptomics) and funcional genomics, we identified genes and molecular networks associated with their mechanism of action and synergy. Our results underlined the clinical potential of these candidates in curbing MCL progression and drug resistance.

overall_design: Cells were treated with YM155 and S63845 as single agents and in combination with PI and BTKi, and RNA was extracted from treated and untreated samples using the Qiagen RNeasy Mini Kit according to manufacturer’s protocol. RNA sequencing was performed (150 bp PE, 20 million reads per sample).

first: Amit K


title: Nanoparticle immunoadjuvant complexes augment antigen-specific germinal center responses

city: Philadelphia

first: David

last: Weiner

state: PA

address: 3601 Spruce Street

institute: The Wistar Institute

summary: A strategy for improving protective humoral immunity against infectious diseases is to directly modulate the germinal center (GC) through immunogen design, such as germline targeting. However, there remains a critical need for next generation vaccine approaches to elicit improved GC responses resulting in increased antibody specificity, diversity, and durability. Here, we investigated whether a cytokine could be scaffolded on nanoparticles to enhance antigen-specific GC responses and drive maturation of B cell lineages. We designed a chimeric nanoparticle using the GT8-60mer, a germline-targeting HIV immunogen, as a model to scaffold IL-21, a canonical GC cytokine. Delivered using plasmid DNA, nanoparticle immunoadjuvant complexes (NICs) scaffolding GT8 and IL-21 (GT8-IL-21-NIC) drove improved serum antibody titers, antigen-specific GC B cells, and functional Tfh cell responses relative to antigen-only nanoparticles and to co-delivery of IL-21 monomer. Immunization with the GT8-IL-21-NIC also improve humoral immune response durability, with improved bone marrow plasma cell responses. Transcriptomic analysis of GT8-specific GC B cells from GT8-IL-21-NIC immunized mice demonstrated upregulation of selection-associated gene signatures. Utilizing mice harboring human VRC01-class bnAb precursor heavy and light chain genes, immunization with the GT8-IL-21-NIC led to enhanced GC responses with increased antibody diversity, clonal expansion, and somatic hypermutation, with B cells acquiring an increased number of key VRC01-class broadly neutralizing antibody mutations. Thus, generating NICs using IL-21 may provide value as a tool to improve antigen-specific GC responses and vaccine-induced immunity.

overall_design: Single-cell V(D)J sequencing of lymph node B cells from VH1-2RJH2/VK1-33RCSd/hTdT mice. Mice were immunized with the GT8-60mer (DNA vaccine) or with GT8-IL-21-NIC (DNA vaccine). Lymph nodes were collected 7 days post immunization, processed, and GT8-specific GC B cells were sorted for 10x Genomics V(D)J library preparation, generating both raw sequencing reads (FASTQ) and processed Cell Ranger V(D)J outputs for each sample.

first: Colby

middle: J

last: Agostino

first: Nicholas

last: Tursi

middle: B


title: Growth of Gaeumannomyces tritici and Gaeumannomyces hyphopodioides in liquid medium after 4 days.

city: Harpenden

first: Erika

last: Kroll

address: West Common

country: United Kingdom

institute: Rothamsted Research

summary: In vitro fungal samples were generated to provide a control for fungal read mapping and to inform future studies into fungal gene expression.

sample_organism:
Gaeumannomyces tritici
Gaeumannomyces hyphopodioides

overall_design: Fungal mycelium was grown up in 200 ml conical flasks containing 50 ml Potato Dextrose Broth (PDB) supplemented with 50 μg/ml kanamycin. Flasks were inoculated with 3 x mycelial plugs taken from the leading edge of a two-week old fungal colony growing on Potato Dextrose Agar. Inoculated flasks were placed in a New Brunswick™ Innova® 44 orbital shaker at 20 °C, 160 RPM for four days. Five flasks were set up for each fungus to provide five treatment replicates.

first: Tania

last: Chancellor

first: Dan

last: Smith

first: Wanxin

last: Chen

first: Eudri

last: Venter

first: Kirstie

last: Halsey

first: Gail

last: Canning

first: Javier

last: Palma-Guerrero

first: Kim

last: Hammond-Kosack

first: Stella

last: Moren-Rosado

first: Rowena

last: Hill

first: Rachel

last: Rusholme Pilcher

first: Neil

last: Hall

first: Mark

last: McMullan


title: Friedreich’s ataxia transcriptomic dysregulation and identification of cell type-specific biomarkers: A systematic review and meta-analysis

city: Wollongong

first: Marnie

last: Maddock

state: NSW

address: Northfields Ave

department: Molecular Horizons, School of Medical and Indigenous Health Sciences

country: Australia

institute: University of Wollongong

summary: Friedreich’s ataxia (FRDA) is a progressive neurodegenerative disease caused by a guanine-adenine-adenine (GAA) trinucleotide repeat expansion within the first intron of the FXN gene. The GAA expansion in FRDA induces a transcriptionally repressive state that reduces expression of the protein product Frataxin. Despite Frataxin's ubiquitous expression, the dorsal root ganglia sensory neurons (SNs) are particularly affected, causing sensory/proprioceptive loss, while lower motor neurons (LMNs) are largely spared in FA. The basis for this cell-type specific selective vulnerability remains a central unanswered question in FRDA pathophysiology. Here we generated induced pluripotent stem cell derived sensory neurons, lower motor neurons and neural crest cells from FRDA and isogenic corrected control cell lines. These were profiled using bulk RNA sequencing and used in the systematic review and meta-analysis of all human bulk RNA-seq datasets derived from FRDA and control samples. Our group performed a systematic review and meta-analysis of human bulk RNA-sequencing datasets in FRDA, reprocessing all studies through a unified analysis pipeline to enable direct cross-study comparison. We analysed 23 independent datasets comprising 94 FRDA and 99 control samples across 10 distinct cell types, spanning both disease-relevant (cardiomyocytes, sensory neurons) and unaffected cell types (fibroblasts, lymphocytes) of FRDA. This integrative approach allowed us to identify transcriptional changes that are consistently associated with FRDA across studies, while simultaneously delineating those that are cell-type specific. We have identified a panel of robust biomarkers of FRDA that would be useful readouts in in vitro drug screens, in clinical trials, as well as generating hypothesis as to how these biomarkers relate to the pathophysiological mechanisms of FRDA. All biomarkers, datasets and results can also be explored through the open-access FRDA Transcriptomic Atlas (https://marniemaddock.github.io/FRDATranscriptomicAtlas/).

overall_design: Bulk RNA-seq profiling of iPSC-derived sensory neurons (SNs), neural crest cells (NCCs) and lower motor neurons (LMNs) from Friedreich's ataxia (diseased [FA1/FA2]) and control (isogenic corrected [FA1ic/FA2ic]) cell lines.

middle: L

first: Sara

last: Miellet

first: Amy

last: Hulme

first: Mirella

last: Dottori


title: A transcription regulator atlas identifies TOX3 as an Atoh1 co-activator in cerebellar development and tumorigenesis

city: SAN FRANCISCO

first: Xiaoxin

state: California

address: 555 mission bay blvd. south, RM382A

department: Cardiovascular Research Institute

institute: University of California, San Francisco

summary: Organ development and function are orchestrated by intricate transcriptional circuits. Here, we present a comprehensive atlas profiling 1,904 transcription regulators in the brain, cerebellum, heart, kidney, liver, ovary, and testis of fetal, neonatal and adult mice. Using this dataset, we uncover TOX High Mobility Group Box Family Member 3 (TOX3) as a potential co-activator of Atoh1 in cerebellar granule neuron progenitors. Tox3-deficient mice display severe ataxia and cerebellar hypoplasia, driven by depletion of granule neuron progenitors, diminished Atoh1 expression, and impaired primary cilia. Single-nucleus RNA-seq analyses reveals compromised maintenance of the progenitor pool. TOX3 is also highly expressed in subsets of medulloblastoma, and its deletion reduces cerebellar neoplasia and prolongs survival in a mouse model. Mechanistically, how lineage-defining factors such as Atoh1 drive robust gene expression despite weak intrinsic transactivation activity remains unclear. We show that Tox3 physically associates with Atoh1 and co-occupies shared regulatory elements, converting an otherwise weak single-copy Atoh1-reponsive E-box into a highly active enhancer that drives transcriptional activation by up to 120-fold, including at an ultra-conserved E-box downstream of Atoh1 itself. Cross-species single-cell comparisons further show an association between Tox3 expression and cerebellum expansion during vertebrate evolution. Together, this work supports Tox3 as a critical Atoh1 co-activator in cerebellar development, tumorigenesis and evolution, while providing an atlas and screening strategy as a valuable resource for exploring novel transcriptional regulators in organogenesis and tissue physiology.

overall_design: Refer to individual Series

first: Guo

middle: N

last: Huang


title: RNA-seq of human articular chondrocytes after exposure to BMP7-derived peptide p[63-82].

city: maastricht

first: Marjolein

last: Caron

department: Orthopedic Surgery

country: Netherlands

institute: Maastricht University

summary: Osteoarthritis is a degenerative joint disease that can currently only be treated by alleviating pain or, ultimately, by a total joint replacement. The bone morphogenetic protein 7-derived peptide p[63-82] offers a potentially novel molecular treatment option for osteoarthritis. Mapping peptide-induced transcriptomic changes in human articular chondrocytes is expected to help reveal how p[63-82] confers its chondrocyte phenotype modulating bioactivity. To this end,  human articular chondrocytes were isolated from the articular cartilage of patients with late-stage osteoarthritis undergoing total knee arthroplasty (METC approved). Cells were stimulated with 100 nM p[63-82] peptide for 24 hours (or vehicle), after which RNA was isolated, and RNAseq was performed. We found a total of 1976 differentially expressed genes. The p[63-82] peptide induces profound transcriptomic changes in primary human articular chondrocytes. One of the dominant transcriptomic alterations was the differential expression of several collagen-related genes. Many of these collagen-related genes have established roles in cartilage homeostasis. The here-acquired transcriptomic insights provide clues into the therapeutic mechanisms of action of the p[63-82] peptide in human articular chondrocytes.

first: Jessica

last: Steijns

first: Tim

last: Welting


title: Regional Molecular Diversity in Chronic Spinal Cord Injury

city: Rochester

first: Chanil

last: Choi

state: MN

address: 200 First Street SW

department: Physical Medicine and Rehabilitation

institute: Mayo Clinic

summary: The development of next generation cellular and acellular therapies for regenerative repair of the injured spinal cord will benefit from a greater understanding of microenvironment heterogeneity. To address this need, we used genome wide RNA sequencing to illuminate gene expression changes in the spinal cord injury (SCI) epicenter, and in regions above and below, 30 days after contusion-compression (8 g Fejota clip) of the lumbar spinal cord (L1/L3) in adult female C57BL7J mice. Across injury zones, there were more upregulated versus downregulated genes, with the most dynamic changes occurring in the epicenter, followed by the below and above regions. The expression of 52.9% of genes was uniquely changed in epicenter, 6.6% in the below region, and 2.8% in the above region, while 18.3% of differentially expressed genes (DEGs) overlapped across regions. Ingenuity Pathway analysis of epicenter DEGs showed 49 unique pathways, including Type II Diabetes Mellitus, P2Y Purinergic Receptor, Amyotrophic Lateral Sclerosis, JAK family kinases, and pathways related to GABA and Glutamate function. Thyroid Hormone Metabolism II, Serotonin degradation, and Myc-Mediated Apoptosis were enriched in the zone above the epicenter, while the Chondroitin sulfate degradation, the Superpathway of Geranylgeranylipidphosphate and Zymosterol Biosynthesis, and Regulation of Cellular Mechanics by Calpain Proteases were enriched below. There were 100 pathways shared across regions emphasizing fundamental roles for Apoptosis, Cytoskeletal organization, Chemokines, Complement, Prothrombin Activation pathways, Type I Diabetes Mellitus Signaling, and RXR signaling. These findings provide a rich resource of candidate mechanisms for additional validation and the design of targeted therapies to improve recovery after spinal cord injury.

overall_design: RNA-seq profiling of the uninjured spinal cord (UI) and the SCI Epicenter, 3 mm Above and 3 mm Below at 30 days after contusion-compression (8 g Fejota clip) of the lumbar spinal cord (L1/L3) in adult female C57BL7J mice.

first: Chan-Il

first: Ha Neui

last: Kim

first: Hyesook

last: Yoon

first: Maja

last: Radulovic

first: Whitney L.

last: Simon

first: Isobel A.

last: Scarisbrick


title: Phenotypically similar but functionally distinct NK cell populations within the human maternal-fetal interface

city: Brest

first: Marie

last: Frutoso

address: 9 rue Félix le Dantec

country: France

institute: LBAI, UMR1227

summary: Natural Killer cell function within tissues extends beyond exerting cytotoxicity, encompassing a range of functions that are just starting to become fully elucidated. In the context of human placentation, NK cells play a key role in enabling initial placentation, which is associated with the acquisition of tolerance-like properties. If and to which extent NK cells maintain these tolerance-like properties over the course of human pregnancy is still poorly understood. We have employed a single-cell sequencing approach using the BD RhapsodyTM system to study the transcriptomic profile of Natural Killer (NK) cells in the decidual-placental interface (DPI) and the decidua (in comparison to NK cells from the maternal circulating blood and the cord blood). We found that NK cells from both location had similar transcriptional profile with the presence of resident NK cells. Yet, when stimulated in vitro, CD103+CD69+ tissue-resident NK cells exhibited distinct effector function from one another. Together, our findings reveal the presence of distinct functional resident NK cell populations in two anatomically adjacent tissues at healthy full-term pregnancies.

overall_design: Immune cell  characterization utilizing targeted single cell RNA sequencing paired with oligo tagged antibodies using the BD Rhapsody/ AbSeq system. In details, cells from maternal blood, cordblood, DPI and decidua from healthy donors and patients who experienced chorioamnionitis were stained with a cytometry panel and one specific oligo-protein-tag for multiplexing (BD Biosciences SMK). Live, CD45+ immune cells were sorted (using the BD Symphony S6 cell sorter equipped with a 70um nozzle for batches 1 and 2 and the FACSAria III equiped with a 100um nozzle). For batches 1 and 2, Live CD45+ cells were enriched for ILC (CD45+CD19-CD14-CD3-CD127+CD34-), NK cells (CD45+CD19-CD14-CD3-CD127-NKp46+) and myeloid cells (CD45+CD3-CD19-NKp46-HLA-DR+).  For batch 3 CD45+ were sorted without enrichment of specific cell type. After sorting, cells from all donors and tissues were pooled and stained with 56 oligo-proteins. Stained cells were then loaded on the BD Rhapsody cartridges (between 35 - 45,000 cells were loaded per cartridges). Cells from the 1st batch (comprising 2 donors and the 4 tissue types) were split into 4 cartridges and sequenced once. Cells from the 2nd batch (comprising 2 donors and the 4 tissue types) were split into 3 cartridges and sequenced once. Cells from the 3rd batch (comprising 4 donors with DPI only) were split into 4 cartridges and each cartridge was sequenced twice.

first: Martin

last: Prlic

first: Caitlin S

last: DeJong


title: Single-cell sequencing reveals dynamic immune features of paraneoplastic pemphigus in a patient with follicular lymphoma

city: Shanghai

first: Yuxuan

last: Zheng

address: 825 Zhangheng Rd.

institute: Fudan University

summary: Background: Paraneoplastic pemphigus (PNP) is a highly fatal autoimmune blistering disease that commonly occurs in patients with underlying benign or malignant neoplasms. It poses significant challenges for diagnosis and treatment. To date, the cellular and molecular mechanisms underlying the pathogenesis of PNP remain largely unclear. Objective: This study aims to elucidate the cellular and molecular mechanisms of PNP, particularly when it occurs secondary to lymphoma, by analyzing the dynamic immune landscape throughout the course of treatment. Method: We performed single-cell transcriptome sequencing and single-cell T cell receptor (TCR) analysis on peripheral blood mononuclear cells (PBMCs) and bone marrow cells (BMCs) obtained from a patient with follicular lymphoma (FL) accompanied by PNP. Samples were collected at three critical time points: before treatment, during treatment, and after successful treatment. Result: Before treatment, we observed a specific enrichment of ITGAL+ T cells, abnormal γδT cell subtypes, and BCL2+ B cells in PBMCs. Notably, naïve T cells and an abnormal B cell subtype were also enriched in BMCs. The single-cell transcriptome results mapped the lymphoma-associated tumor microenvironment and revealed post-treatment immune reconstitution. This reconstitution involved activated DNA damage and T cell immune responses, which was further supported by the observation of a gradually expanded TCR clone as the treatment progressed. Conclusion: Our study delineates the dynamic immune landscape in a patient with FL-associated PNP throughout treatment, demonstrating that successful treatment correlates with immune reconstitution involving specific T cell responses and TCR clone expansion. These findings provide novel insights into the cellular and molecular mechanisms of PNP, especially in cases secondary to lymphoma.

overall_design:
To decipher the cellular and molecular characteristics and potential mechanisms of the PNP through this case, we performed single-cell multi-omics sequencing, including single-cell RNA-seq (scRNA-seq) and single T cell receptor repertoire sequencing (scTCR-seq), using PBMCs collected from four time points prior- and post-treatment (C0, C1, C2, and C4).

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The raw sequence data reported in this study have been deposited in the Genome Sequence Archive in National Genomics Data Center, China National Center for Bioinformation / Beijing Institute of Genomics, Chinese Academy of Sciences (GSA-Human: HRA016740) that are publicly accessible at https://ngdc.cncb.ac.cn/gsa-human.
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first: Rong

last: Wei

first: Bochao

last: Liu

first: Yun

first: Wenjing

last: Li

first: Zhiguo

last: Chen

first: Jin

last: Lu

first: Shenmiao


title: Resistance-based exercise restores muscle health in dialysis patients

city: Chicago

first: Ajay

last: Rana

state: IL

address: 840 S. Wood Street

department: Surgery

institute: University of Illinois at Chicago

summary: Chronic kidney disease (CKD) and end-stage renal disease (ESRD) are serious health concerns worldwide that require regular dialysis before a kidney transplant for a better quality of life. Due to aging and frailty, kidney dialysis patients are often limited in physical activity, which can lead to multiple health complications and sometimes result in patient death. Therefore, maintaining muscle health is crucial for kidney dialysis. We recently reported that personalized resistance-based exercise can improve frailty in kidney dialysis patients; however, the underlying molecular mechanisms by which resistance-based exercise improves muscle health are unknown. RNA-Seq analysis revealed that exercise promotes the expression of genes related to muscle stemness, regeneration, and differentiation. The IHC analysis revealed increased protein expression of stemness-associated proteins, including Lamin A/C, 5'-adenosine monophosphate-activated protein kinase (AMPK), paired box 7 (PAX7), vascular cell adhesion molecule 1 (VCAM-1), and Emerin. The IF analysis revealed increased protein expression of muscle differentiation markers, including myoblast determination protein 1 (MyoD), myosin heavy chain (MyoH), myogenin, desmin, dystrophin, and enolase 3. Furthermore, our study demonstrated that exercise upregulated proteins such as mitochondrial encoded cytochrome c oxidase III (MTCO3) and aconitase 2 (ACO2), which are involved in the oxidation of organic compounds and mitochondrial function in muscle. Moreover, we observed that exercise increased the protein expression of glucose transporter protein types 1 and 4 (GLUT1 and GLUT-4), glycogen synthase 1 and 2 (GYS1 and GYS2), and fatty acid binding protein 1 (FABP1), which participate in energy production through glucose uptake, glycogenesis, and fatty acid metabolism, respectively. These results suggest that personalized resistance-based muscle therapy in dialysis patients promotes the expression of genes and proteins associated with muscle stemness, regeneration, differentiation, and energy generation.

overall_design: RNA-seq analysis was performed on de-identified skeletal muscle samples collected from dialysis patients before and after 12 months of supervised, resistance-based muscle therapy.

first: Rana

last: Ajay

first: Kumar

last: Sandeep

first: Singh

last: SK

first: Nair

last: RS

first: Srivastava

last: Piush

first: Benedetti

last: Enrico


title: Integrated transcriptomic and metabolomic analyses reveal the regulatory network underlying NtGSTU10-mediated nicotine synthesis and transport in tobacco

city: guiyang

first: yudan

last: zhou

address: West Campus of Guizhou University, Huaxi District

institute: Guizhou University

summary: Nicotine is the major alkaloid in tobacco and plays a key role in determining tobacco quality. Previous studies have shown that overexpression of NtGSTU10 enhances nicotine accumulation in tobacco hybrids; however, the molecular mechanisms underlying this process remain largely unclear.

overall_design: In this study, we investigated the regulatory role of NtGSTU10 in nicotine synthesis and distribution using integrated transcriptomic and metabolomic analyses in NtGSTU10-overexpressing tobacco plants. Nicotine content and distribution between roots and leaves were quantified, and global transcriptional and metabolic profiles were analyzed to reveal molecular changes associated with NtGSTU10 overexpression. The results showed that NtGSTU10 overexpression was associated with increased nicotine accumulation in leaves and reduced nicotine levels in roots, resulting in significantly higher nicotine transport coefficients compared with wild-type plants. Transcriptomic analysis revealed coordinated changes in genes involved in nicotine biosynthesis, transport, and secondary metabolism. Metabolomic profiling indicated significant alterations in amino acid metabolism, nicotinic acid and nicotinamide metabolism, purine metabolism, sugar metabolism, and alkaloid biosynthesis pathways. Integrated transcriptome–metabolome analysis further identified coordinated regulation of glutathione metabolism, ABC transporters, and MATE transporter–encoding genes. Overall, these results reveal a regulatory network associated with NtGSTU10-mediated nicotine biosynthesis and transport, providing new insights into the molecular mechanisms underlying nicotine metabolism in tobacco.

first: Yudan

last: Zhou


title: HER2-Specific Synthetic Antigen Receptor (SAR) T Cell Therapy Synergizes with Radiotherapy to Provide Improved Anti-Tumor Efficacy in Non-Small Cell Lung Cancer (NSCLC)

city: Hamilton

first: Theodoros

last: Tsakiridis

address: 699 Concession St

country: Canada

institute: McMaster University

summary: In non-small cell lung cancer (NSCLC), radiotherapy not only mediates cytotoxicity but also activates radioresistance drivers like HER2. We investigated radiotherapy combined with HER2-targeted T cell therapy in an NSCLC model. The antitumor efficacy of radiotherapy and engineered T cells expressing a DAP12-associated synthetic antigen receptor (SAR) targeting HER2 was evaluated in HER2-expressing A549 xenografts. HER2 modulation, transcriptional regulation, and tumor T cell infiltration were assessed using immunoblotting, realtime quantitative polymerase chain reaction, flow cytometry, RNA-seq, and immunohistochemistry. High-dose HER2-SAR T cell infusion abolished A549 tumor growth but induced graft-vs-host disease. Low-dose T cell infusion was well-tolerated and provided partial tumor inhibition. Induction radiotherapy (7 d before T cell infusion) synergistically improved tumor control and survival. Radiotherapy transiently upregulated HER2 expression (4 to 24 h), though administering HER2-SAR T cells within this window did not enhance antitumor efficacy. Radiation did not enhance T cell-mediated cytotoxicity in vitro. However, in tumors, radiotherapy increased intratumoral proliferation and accumulation of HER2-SAR T cells and enhanced the extrinsic apoptotic pathway, including induction of Fas transcript and protein levels and cleaved caspase-3 (CC3). RNA-seq of irradiated tumors revealed lasting transcriptional reprogramming with increased immune activation and decreased proliferation and oncogenic signaling. Induction radiotherapy enhances HER2-SAR T cell infiltration and provides synergistic tumor suppression, likely through additional activation of immune-mediated apoptosis. These findings support further assessment of HER2-SAR T cell therapy in HER2-expressing NSCLC.

overall_design: Total RNA was isolated from enhanced firefly luciferase (Luc)-expressing A549 tumors grown in NRG mice. Tumors from three biological replicates were treated with either 0Gy (control) or 5Gy (treatment) radiotherapy and harvested either 24h or 7 days post-treatment. In total, 12 samples were analyzed: 3x24h post-0Gy, 3x24h post-5Gy, 3x7d post-0Gy and 3x7d post-5Gy.

first: Olga-Demetra

last: Biziotis

first: Christopher

middle: M

last: Silvestri

first: Allyson

last: Moore

first: Russta

last: Fayyazi

first: Simon

last: Wang

first: Elham

last: Ahmadi

first: Daniel

last: Del Rosso

first: Amr

last: Ali

first: Evangelia

last: Baker

first: Craig

last: Aarts

first: Bojana

last: Bojovic

first: Joanne

middle: A

last: Hammill

first: Gregory

middle: R

last: Steinberg

first: Jonathan

last: Bramson


title: Single-cell RNA-seq analysis of human iPSC-derived lung organoids

city: Seoul

first: Eun-mi

last: Kim

address: 621, Hwarang-ro

country: South Korea

institute: Seoul Women's University

summary: This study presents single-cell RNA sequencing data from human induced pluripotent stem cell (hiPSC)-derived lung organoids. The data characterize transcriptional diversity in lung organoids.

overall_design: Human lung organoids were differentiated from hiPSCs. Single-cell suspensions were captured using the 10x Genomics Chromium platform, and libraries were sequenced on Illumina NovaSeq 6000.

first: Seung-Yeon

first: Jo-Won

last: Baek

first: Eo Jin

first: Sathiyaraj

last: Srinivasan

first: Kee K.

first: Eun-Mi


title: Oncogenic and tumor-suppressive forces converge on a progenitor-orchestrated niche to shape early tumorigenesis [kras_inhibitor_scRNA-seq]

city: New York

first: Yu-Jui

last: Ho

address: 417 E 68th St

institute: Memorial Sloan Kettering Cancer Center

summary: The transition from benign to malignant growth is a pivotal yet poorly understood step in cancer progression that marks the shift from a pathologically inert condition to a clinically lethal disease. Here, we integrate lineage tracing, single-cell and spatial transcriptomics to visualize the molecular, cellular and tissue-level events that promote or restrain malignancy during the tumor initiation in mouse models of pancreatic ductal adenocarcinoma (PDAC). We identify a discrete progenitor-like population of KRAS-mutant cells that co-activates oncogenic and tumor-suppressive programs—including p53, CDKN2A, and SMAD4—engaging senescence-like responses and remodeling their microenvironment, ultimately assembling a niche that mirrors invasive PDAC. Even brief KRAS inhibition in the epithelial compartment depletes progenitor-like cells and dismantles their niche, substantially delaying cancer initiation. Conversely, p53 suppression enables progenitor cell expansion, epithelial–mesenchymal reprogramming, and immune-privileged niche formation. These findings position the progenitor-like state as the convergence point of cancer-driving mutations, plasticity, and tissue remodeling—revealing a critical window for intercepting malignancy at its origin.

overall_design: To assess the consequences of acute oncogenic Kras inhibition on the spectrum of pancreatic premalignant states in the context of pancreatic injury, we subjected 5-week-old KPLOH (Ptf1a-Cre; LSL-KrasG12D; Rosa26-CAGS-LSL-rtTA3-IRES-mKate2; p53flox/wt; TRE-GFP-shRen.713) mice to eight-hourly intraperitoneal injections of 80 μg kg-1 of caerulein (Bachem) for two consecutive days (16 injections total). In addition, we treated mice with MRTX1133 (30mg/kg) or vehicle concurrently with caerulein treatment, euthanizing mice within 4 h of the last MRTX1133 or vehicle dose (fifth dose, 2 days after the first dose).

first: José

last: Reyes

first: Scott

last: Lowe

first: Dana

last: Pe'er


title: Comprehensive mass spectrometry screening-derived atlas of HDAC inhibitors revelas histone specific acetylation chnages [RNA-seq]

city: St. Louis

first: Rashmi

last: Karki

address: 660 S. Euclid Ave

institute: Washington University in St. Louis

summary: Histone deacetylases inhibitors (HDACi) have emerged as valuable therapeutics in cancer and other diseases, yet their effect on histone post-translational modification remains incompletely characterized. Here, we applied quantitative mass spectrometry and high throughput sequencing to systematically profile site-specific histone modification changes in response to a panel of HDAC inhibitors. This platform enabled mapping of histone modification changes across hundreds of sites including low abundant histone marks. Furthermore, integrative analysis of ChIP-seq and RNA-seq identified genome wide binding site for a low-abundant histone mark H2A.Z acetylation in HeLa cells and MDA-MB-231 breast cancer cells, highlighting the role of H2A.Z acetylation in regulating gene expression through various biological pathways and specific genes involved in tumor suppressor pathways. Our findings provide a functional resource for identification and quantification of epigenetic changes and transcriptional regulation of histone H2A.Z acetylation upon pharmacological perturbation

overall_design: RNA-seq profiling for HeLa and MDA-MB-231 cells treated with Entinostat (1uM) for 24h. Controls were treated with DMSO. Two replicates were included for  each conditions.

first: Francisca

last: Vitorino

first: Richard

last: Searfoss

first: Joanna

middle: K

last: Lempiäinen

first: Benjamin

last: Garcia

first: Cheryl

last: Arrowsmith


title: Deep-learning Analysis of 3D Microarchitectural Remodeling in Hypertrophic Cardiomyopathy

city: Boston

first: Jonathan

last: Seidman

state: Massachusetts

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

summary: Hypertrophic cardiomyopathy (HCM), a genetic heart disease defined by unexplained cardiac wall thickening, is a leading cause of sudden death worldwide. However, the three-dimensional organization of cardiac tissue underlying left ventricular hypertrophy remains poorly understood. We developed CaMVIA-3D, a deep-learning volumetric imaging and analysis pipeline to characterize cardiac microarchitecture. Analysis of tissues from HCM hearts revealed genotype-specific differences in cardiomyocyte volume, morphology, and extracellular volume, with pathogenic variants exhibiting greater concentric cellular hypertrophy and disarray, and variant-negative cases showing predominant fibrosis. Longitudinal profiling of a pig HCM model revealed early-onset fibrosis preceding cardiomyocyte hypertrophy. Integrating transcriptomic and morphologic changes, we identified genes associated with cellular and extracellular remodeling. These findings define genotype-specific microstructural differences in HCM, offering insights to improve diagnostics and targeted therapies.

overall_design: We analyzed snRNA-seq data and volumetric measurements from left ventricular free wall tissue of R403Q and wild-type pigs to investigate molecular signals of cardiomyocyte hypertrophy and extracellular remodeling. Nuclei from 33 animals were isolated, sequenced, and quality controlled; data were integrated with Harmony and visualized by UMAP. Canonical markers defined 10 major cardiac cell types, including cardiomyocytes and fibroblasts. Gene expression analyses and elastic net regression identified associations between highly expressed genes and microstructural features (cardiomyocyte volume, width, and extracellular volume), which were validated by correlation analyses.

first: Eric Q

last: Wei

first: Martin

last: Beyer

first: Kemar J

last: Brown

first: Alexander J

last: Bansbach

first: Joshua

last: Gorham

first: Barbara

last: McDonough

first: Huachen

last: Chen

first: Mobin

last: Khoramjoo

first: Anran

last: Zhang

first: Brian

last: Bishop

first: Ferhaan

last: Ahmad

first: Carlos

last: del Rio

first: Ching-Pin

last: Chang

first: David M

last: Ryba

first: Sharlene M

last: Day

first: Diane

last: Fatkin

first: Gavin Y

last: Oudit

first: Christine E

first: Jonathan G


title: CD63 regulates corneal epithelium abundant genes in the limbus

city: Seattle

first: Yuzuru

last: Sasamoto

state: WA

address: 750 Republican St

department: Ophthalmology

institute: University of Washington

summary:
PURPOSE.  Building on identification of ABCB5 as a limbal stem cell (LSC) marker, this study evaluates CD63, a newly identified LSC molecule co-expressed with ABCB5, in human limbal epithelial cells to elucidate its role in maintaining corneal epithelial identity.
METHODS. RNA sequencing (RNA-seq) was performed on sorted Abcb5-positive and Abcb5-negative murine corneal epithelial cells. CD63 expression in human corneal tissue was assessed by flow cytometry and immunostaining. siRNA-mediated knockdown (KD) of CD63 was conducted in cultured human limbal epithelial cells. Subsequent analyses included qRT-PCR, flow cytometry, RNA-seq, and western blotting.
RESULTS. RNA-seq analysis of mouse corneal epithelial cells revealed high expression of LSC markers, including Krt15, Krt6b, Fgfr1, Gpha2, Ifitm3, and Cd63, as well as low expression of differentiation-associated markers, such as Krt12 and Gja1, in Abcb5-positive cells. In human corneal tissue, flow cytometry and immunostaining confirmed robust CD63 expression in the limbal region. siRNA-mediated KD of CD63 in cultured human limbal epithelial cells resulted in a marked reduction in the expression of corneal epithelium-enriched genes, including KRT12, CLU, ALDH1A1, ALDH3A1, TGFBI and MYEOV. Notably, CD63 KD resulted in a ~50 % decrease in expression of a key transcriptional regulator of corneal epithelial identity, PAX6.
CONCLUSIONS. CD63 is abundantly expressed in the human limbus and plays a critical role in maintaining the expression of corneal epithelium-specific proteins, likely through modulation of PAX6. These findings underscore the functional significance of CD63 in limbal stem cell biology and its essential contribution to corneal epithelial homeostasis.

overall_design:
Comparative gene expression profiling analysis of RNA-seq data. We used mouse and human samples. (1) For mouse, we purified Abcb5-positive and -negative corneal epithelial cells by flow cytometry. (2) For human, we used cultured limbal epithelial cells treated with siRNAs (Control, CD63 knockdown #1, and CD63 knockdown #2).

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

last: Lee

first: Gabrielle

last: Martin

first: Bruce

last: Ksander

first: Markus

last: Frank

first: Natasha

middle: Y


title: Unconventional role of HMGCS1 in driving pathogenic-Th17 cell immunity and autoimmune diseases [scRNA-seq]

city: Wuhan

first: Jie

last: Sun

state: Hubei

address: Donghu Road, No. 115

department: MRI

institute: Wuhan university

summary: Identifying factors controlling pathogenic-Th17 cells is of importance, for their vital role in inflammation and immune-pathology. While intricate ER stress signals have been implicated in T cell biology, its role in Th17 cells remain poorly understood. Here, we demonstrated that HMGCS1, a cholesterol biosynthesis precursor enzyme, was highly induced by inflammatory cytokines and preferentially expressed by pathogenic-Th17 cells in vitro and in vivo. HMGCS1 specifically dictated pathogenic-Th17 cell differentiation and augmented autoimmune diseases. Nonetheless, HMGCS1 role in pathogenic-Th17 cells was independently of cholesterol metabolism but necessitated its catalytic Cys129 residue. Notably, HMGCS1 leveraged IRE1a-XBP1s-dependent ER stress response which was essential for pTh17 cell generation and pathogenicity by transcriptionally activating Rorc loci. Mechanistically, HMGCS1 located to the ER membrane, where it bound and stabilized IRE1a protein via restraining IRE1a interaction with K48-linked ubiquitination-dependent E3 ligase MARCH5. Of note, interfering HMGCS1 and ER stress impeded pathogenic-Th17 immunity and mitigated autoimmune diseases. Therefore, our work reveals a non-canonical axis wherein HMGCS1 sustains ER stress to license pTh17 cell differentiation during autoimmune responses.

overall_design: Wild-type C57BL/6 mice were induced with Experimental Autoimmune Encephalomyelitis (EAE) using MOG35-55 peptide. Draining lymph nodes (dLNs) and spinal cords were isolated at the peak of the disease.

first: Bing

last: Wu


title: Vip+ Vagal Neurons Control Allergen-Induced Responses

city: San Diego

first: Ziai

last: Zhu

address: 9500 Gilman Dr

institute: UCSD

summary: RNA sequencing of vagal ganglia following repeated allergen exposure revealed widespread transcriptional changes, providing insights into how vagal sensory neurons adapt to chronic inflammatory stimuli.

overall_design: Vagal ganglia isolated from saline- and HDM- treated mice were collected at 1.5 h after the fourth challenge. For each biological replicate, 6-8 ganglia from 3-4 mice were pooled.


title: Genome-wide CRISPR sgRNA loss-of-function screening in PRCC-TFE3 inducible HK-2 cells

city: Kumamoto

first: Masaya

last: Baba

state: Kumamoto

address: 1-1-1 Honjo, Chuo-ku

department: Urology

country: Japan

institute: Kumamoto University

summary: PRCC-TFE3 is an oncogenic chimeric transcription factor that drives TFE3-rearranged renal cell carcinoma. Although PRCC-TFE3 can trigger either oncogene-induced senescence (OIS) or tumor progression depending on the cellular context, both phenotypes are fundamentally dependent on its transcriptional function. This study aims to identify genetic factors essential for the transcriptional activity and functional output of PRCC-TFE3. Using a doxycycline (Dox)-inducible PRCC-TFE3 HK-2 cell model where the fusion protein induces robust OIS, we performed a genome-wide CRISPR/Cas9 knockout screen. By identifying genes whose loss alleviates this OIS phenotype, we sought to uncover key regulators required for PRCC-TFE3-mediated transcriptional programs.

overall_design: A genome-wide CRISPR/Cas9 screen was conducted using the Brunello library in two independent experimental runs performed at different times. Each run consisted of a paired comparison between PRCC-TFE3 non-induced (Dox−) and induced (Dox+) conditions in HK-2 cells. Run 1: Pair of Doxy-_1 (control) and Doxy+_1 (PRCC-TFE3 induced). Run 2: Pair of Doxy-_2 (control) and Doxy+_2 (PRCC-TFE3 induced). Because PRCC-TFE3 induction in this cell model enforces OIS via its transcriptional activity, loss of genes required for PRCC-TFE3 function allows cells to bypass senescence and gain a growth advantage. sgRNA abundance was quantified by NGS, and differential enrichment between the paired populations was analyzed using the MAGeCK pipeline to identify essential mediators of PRCC-TFE3-mediated functional programs.

first: Hidekazu

last: Nishizawa

first: Shintaro

last: Funasaki

first: Shoichiro

last: Kuroda


title: RNA-seq analysis of PRCC-TFE3 dependent transcriptional programs and their modulation by MSC2530818 in HK-2 cells.

summary: PRCC-TFE3 is an oncogenic chimeric transcription factor identified in TFE3-rearranged renal cell carcinoma. To characterize PRCC-TFE3–dependent transcriptional programs and their regulation by the Mediator kinase module, we performed RNA sequencing in a doxycycline-inducible PRCC-TFE3 expression system. HK-2 cells expressing HA-tagged PRCC-TFE3 under doxycycline control were cultured under four conditions defined by the presence or absence of doxycycline and the CDK8/19 inhibitor MSC2530818. RNA-seq was conducted to assess global gene expression changes associated with PRCC-TFE3 induction and CDK8/19 inhibition. These data provide a resource for analyzing PRCC-TFE3–driven transcriptional reprogramming and its modulation by the Cyclin C–CDK8/19 Mediator kinase module.

overall_design: PRCC-TFE3 doxycycline (Dox)-inducible HK-2 cells were cultured for 48 h under four conditions defined by the presence or absence of Dox and the CDK8/19 inhibitor MSC2530818 (100 nM). Three independent biological replicates were analyzed for each condition.


title: Unconventional role of HMGCS1 in driving pathogenic-Th17 cell immunity and autoimmune diseases II

overall_design: Naive CD4+ T cells, which were purified from spleen and lymph nodes, were cultured under npTh17 and pTh17  polarization conditions from WT for 2 days. Then, RNA was extracted from the npTh17 and  pTh17 cells.


title: Retinal Organoid Screening Reveals ABT-737 and Luminespib as Selective Agents Against Tumorigenic Cone Precursors in Retinoblastoma

city: Newcastle University

first: Majlinda

last: Lako

address: Newcastle University

institute: Newcastle University

summary: Retinoblastoma (Rb) is primarily driven by proliferating cone precursors, particularly those in the G2/M phase, as revealed by recent single-cell transcriptomic studies. In this study, we utilized patient RB1⁻/⁻ retinal organoids to evaluate the cytotoxic efficacy and selectivity of candidate therapeutics targeting these tumor-initiating cells. A primary screen of 37 compounds identified 11 with significant cytotoxicity, which was subsequently refined to six candidates exhibiting selective activity against proliferating cone precursors. Among these, ABT-737 and Luminespib emerged as lead compounds, demonstrating dose-dependent depletion of Ki-67⁺/RXRγ⁺ cone cells and strong apoptotic induction—evidenced by Caspase-3 activation and Annexin V/7-AAD flow cytometry—without inducing necrosis. Single-cell RNA sequencing confirmed that both agents selectively ablated the Rb-like proliferating cone precursors. Ocular pharmacokinetic modeling using pluripotent stem cell-derived RPE monolayers revealed limited permeability across the outer blood-retinal barrier for both drugs; however, Luminespib showed moderate translocation, likely due to its lower molecular weight. Together, these findings highlight ABT-737 and Luminespib as promising, selective therapeutic candidates for Rb and demonstrate the utility of integrated retinal organoid and RPE models for preclinical drug screening and pharmacokinetic evaluation.

overall_design: In this study, we utilized patient RB1⁻/⁻ retinal organoids to evaluate the cytotoxic efficacy and selectivity of candidate therapeutics targeting these tumor-initiating cells. A primary screen of 37 compounds identified 11 with significant cytotoxicity, which was subsequently refined to two  candidates exhibiting selective activity against proliferating cone precursors.

first: Joe

last: Kelk

first: Agata

last: Rozanska

first: Eleni

last: Sotiriadou

first: Dan

last: Astley

first: Rafiqul

last: Hussain

first: Adrienne

last: Unsworth

first: Abbie

last: Gangar

first: Archie

last: Robinson

first: Rachel

last: Queen

first: Jon

last: Hardcastle

first: Gareth

last: Veal


title: Optic Nerve Head Spatial Transcriptomic Change in Non-Human Primate Early Experimental Glaucoma.

city: Portland

first: Priya

last: Chaudhary

state: OR

address: 1225 NE 2nd Avenue

department: Devers Eye Institute

institute: Legacy Research Institute

summary:
Purpose: To determine optic nerve head (ONH) laminar collagen and retrolaminar myelin expression change in non-human-primate (NHP) experimental-glaucoma (EG) using immunohistochemistry (IHC) and spatial transcriptomics.
Methods: Unilateral EG NHPs (n=3) were perfusion fixed, ONHs were trephined, embedded in paraffin and serial sectioned for IHC and spatial transcriptomics. EG versus control eye retinal nerve fiber layer thickness (RNFLT) and axon loss within each region of study were estimated.
Results: CNPase levels decrease in the retrolaminar region of the ONH in early EG by IHC. Multiple myelin genes are decreased in early NHP EG in the retrolaminar region. Inflammatory pathways were upregulated in the retrolaminar region as well. Among the top genes that were altered in the laminar region were collagen related genes and Transforming Growth Factor Beta 1 (TGFβ1).
Conclusions: Spatial transcriptomics analysis revealed a consistent downregulation of multiple myelin-related genes, while IHC confirmed a corresponding decrease in CNPase protein expression. Importantly, spatial transcriptomics identified differential profiles among the prelaminar, laminar, and retrolaminar ONH. Together, these findings highlight early myelin disruption and provide insights into the spatial and molecular dynamics of disease onset in NHP. This work advances our understanding of glaucoma pathogenesis and lays the groundwork for developing novel therapeutic strategies.

overall_design: GeoMx DSP results of ROIs that includes prelamina, lamina, retrolaminar regions from control and experimental glaucoma eyes.

first: Galen

last: Williams

first: Jinho

last: Lee

first: Gabriel

last: Zangirolani

first: Juan

last: Reynaud

first: Hongli

last: Yang

first: Nicholas

last: Marsh-Armstrong

first: Claude

last: Burgoyne


title: Oncogenic and tumor-suppressive forces converge on a progenitor-orchestrated niche to shape early tumorigenesis [Multiome-seq]

first: Yu-Jui

last: Ho

overall_design: To assess the spectrum and dynamics of premalignant states and tissue remodeling events in the in the context of oncogenic KRAS activation in the premalignant epithelium, we subjected 5–6-week-old male mice with eight-hourly intraperitoneal injections of 80 μg kg-1 of caerulein (Bachem) for two consecutive days (16 injections total). Caerulein dose was adjusted to body weight at the beginning of each day of treatment. We harvested the pancreata at 2 days after the first caerulein injection, collecting single cells for single cell RNA and ATAC multiome analysis.

first: José

last: Reyes

first: Scott

last: Lowe

first: Dana

last: Pe'er


title: High altitude de-acclimatization leads to long-term immune-suppression via upregulating Nrf2 expression in Tregs

city: Beijing

first: Zhijie

last: Bai

state: 北京Beijing

address: Taiping Road, Haidian District

institute: beijing institute of radiation

summary: Introduction: High-altitude exposure imposes hypoxic, low-pressure, and cold conditions that challenge immune homeostasis. The long-term effects of high-altitude de-acclimatization (HADA) remain poorly understood. Objectives: The purpose of this study is to investigate how HADA affects the immune populations, both quantitatively and functionally, and to dissect the underlying molecular mechanisms involved. Methods: Peripheral blood was collected from both human cohorts and mice models while other immune organs including spleen, thymus and bone marrow were obtained from mice models. Proportions of immune cell populations in peripheral blood and other immune organs were analyzed using flow cytometry. The immune-suppressive functions of Tregs were determined by in vitro co-culture with CD8+ T cells. Transcriptomic and chromatin-accessibility feature induced by HADA were obtained through RNA-seq and ATAC-seq. The functional validation of HADA target gene was performed using specific agonist during in vitro co-culture. Results: HADA perturbed the proportions of immune populations in multiple immune site. Both data from human and mice showed increased regulatory T cells (Tregs) and enhanced immune-suppressive function in the peripheral blood. As a consequence, these Tregs mediated long-term immune suppression, impairing the immunity against tumor cells. Multi-omic analyses predicted Nrf2 as the key mediator of molecular alterations in Tregs caused by HADA, which was further confirmed by the functional assay. Conclusion: High-altitude de-acclimatization mediates the expansion of peripheral Tregs and enhances long-lasting immunosuppressive function of Tregs, increasing the probability of serious health consequences. Nrf2 plays as a key regulator mediating the effects of HADA on Tregs. These findings provide novel insights into altitude-related immune regulation and implications for health management in populations transitioning between high and low altitudes.


title: Endogenous retroviral elements LTR8B and MER65 regulate the PSG9 locus that promotes trophoblast syncytialization: Insights into placental evolution and pre-eclampsia pathology

city: Paris

first: Manvendra

last: Singh

address: 160 Rue de Vaugirard,

department: Systems Biology

institute: Institut Necker

summary: Understanding the causes of the exceptional rate of evolution of the mammalian placenta is likely to aid the understanding of placental development and the aetiology of the human-specific pregnancy disorder pre-eclampsia (PE). As retroelements (REs) are often lineage-specific and known to be co-opted for placental functioning, here we consider the RE binding of GATA3 and DLX5, these transcription factors being dysregulated in PE, and their downstream consequences. Here we identify that the LTR8B cCREs facilitates the binding of transcription factors (e.g., GATA3, DLX5, TFAP2A/C), resulting in a diversified PSG gene expression pattern within a primate-specific genomic region that exhibits high intraspecies variability. The LTR8B/PSG9 regulatory element influences other PSG family members. PSG9, unique among PSGs, produces both secreted and membrane-anchored isoforms, MER65-int providing alternative polyA signals, enabling the evolution of secreted PSG variants through the truncation of the ancestral CEACAM protein’s transmembrane domain. The LTR8B/PSG9 locus regulates the differentiation of multinucleated trophoblasts (syncytialization) and, like chorionic gonadotropin and syncytin1, determines the identity of syncytiotrophoblasts. Notably, PSG9 is the most upregulated PSG in PE, with levels correlated with GATA3 and DLX5 levels. Altogether, REs contribute to the structural and expression evolution of PSG genes, facilitating lineage-specific placental evolution. The LTR8B/PSG9 regulatory network plays a central role in syncytiotrophoblast differentiation. Given the association between DLX5/GATA3 dysregulation and elevated PSG9 levels, along with PSG9’s expression in the first trimester, PSG9 shows potential as a predictive biomarker for PE.

overall_design: For LTR8BKO, wild type control and LTR8B KO BeWo cells were seeded in 6-well plate at the concentration 1 x 10^6 cells per well of 6-well plate. At 2nd day, cells were treated with 50 μM Forskolin for 48h. Then cells were harested for RNA extraction and downstream bulk RNA-seq. For PSG9 KD, BeWo cells were seeded in 6-well plate at the concentration 1 x 10^6 cells per well of 6-well plate. At 2nd day, cells were transfected with ~ 2,5 μg pLKO.1-scramble or ~ 2,5 μg pLKO-PSG9shRNA by the Lipofectamine 3000 reagent. At 24h post-transfection, transfected cells were screened with the fresh media containing 4 μg/ml Puro for 24h. Then transfected cells were washed and further treated with the mixture of 50 μM Forskolin and 4 μg/ml Puro for 48h. Cells were harvested for RNA-seq analysis. In the end, 3 representative replicates were selected for RNA-seq based on the RNA quality.

first: Zsuzsanna

last: Izsvák

first: Yuliang

last: Qu

first: Julianna

last: Zadora


title: Oncogenic and tumor-suppressive forces converge on a progenitor-orchestrated niche to shape early tumorigenesis

department: Cancer Biology & Genetics Program

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

overall_design: Refer to individual Series


title: PTPN2 deficiency amplifies interferon signaling and impairs functional maturation of human stem cell-derived islets [RNA-Seq]

city: Anderlecht

first: Valerie

last: Vandenbempt

state: Vlaams-Brabant

address: Lenniksebaan 808

country: Belgium

institute: Université Libre de Bruxelles

summary: Background: Protein tyrosine phosphatases (PTPs) play key roles in b-cell function and diabetes development. PTPN2 is a candidate gene for type 1 diabetes (T1D) that negatively regulates the JAK/STAT signaling. However, the impact of PTPN2 deficiency on the differentiation and functionality of human stem cell-derived somatic metabolic cells remains unclear.  Methods: PTPN2 expression in b cells from T1D organ donors and during the differentiation of human stem cell-derived islets (SC-islets) was evaluated in single-cell RNA-Sequencing data. Moreover, we differentiated CRISPR-Cas12a genome-edited PTPN2-deficient H1 human embryonic stem cells (H1-hESCs) into SC-islets, and sc RNA-Seq was performed. The maturation and functionality PTPN2 deficient SC-islets were assessed by implantation under the kidney capsule of NOD-SCID mice. Results: scRNA-Seq analysis showed that PTPN2 expression was increased in b cells from recently diagnosed T1D and decreased in long-standing T1D organ donors, compared with controls. Conversely, we found that PTPN2 expression was decreased at early stages of SC-islet differentiation and reconstituted at later stages, suggesting a developmental dynamic. CRISPR/Cas12-mediated gene editing was used to generate PTPN2-knockout human embryonic stem cells. PTPN2 deficiency exacerbated interferon-induced inflammatory signaling in stem cells and differentiated somatic metabolic cells. Interestingly, PTPN2 deficiency increased hedgehog signaling and reduced SC-islet differentiation efficiency in vitro. In addition, PTPN2-knockout SC-islets exhibited reduced glycemic control after implantation in vivo, mediated by reduced cell endocrine identity and enhanced interferon signaling. Conclusions: Our study postulates a key role of PTPN2 in preserving b-cell function during inflammatory and metabolic stress in SC-islets.

overall_design: ATAC sequencing on stem cells with or without PTPN2 under IFNg treatment

first: Javier

last: Negueruela

first: Francisco

last: Ribeiro-Costa

first: Mariana

last: Nunes

first: Leonardo

last: Traini

first: Sema Elif

last: Eski

first: Wadsen

last: Saint-Pierre-Wijckmans

first: Stéphane

last: Demine

first: Nicolas

last: Baeyens

first: Hazem

last: Ibrahim

first: Luciano

middle: G

last: Martelotto

first: Sumeet Pal

first: Alessandra

last: Cardozo

first: Esteban

last: Gurzov


title: Exposure of male mice to nicotine leads to metabolic dysfunction in their male and female offspring

city: Irvine

first: Raquel

last: Chamorro-Garcia

address: 4351 Natural Sciences 2

institute: University of California Irvine

summary: Paternal exposure to nicotine has been linked to altered metabolic phenotypes in offspring, yet the underlying mechanisms and sex-specific outcomes remain elusive. In this study, we investigated the effects of paternal nicotine exposure on glucose metabolism, and adipose tissue and liver transcriptomic profiles in male and female offspring. Despite no differences in body weight during early postnatal life, female offspring displayed lower fasting glucose and reduced glucose levels during glucose tolerance tests, without alterations in insulin sensitivity. These effects were accompanied by decreased circulating insulin and upregulation of genes involved in the insulin signaling pathway in gonadal white adipose tissue (gWAT), consistent with enhanced glucose uptake capacity. In contrast, male offspring showed no overt changes in glucose tolerance or insulin sensitivity, despite reduced plasma insulin and glucagon levels. In male offspring, liver transcriptomic analyses revealed downregulation of glucagon signaling, insulin resistance, and PPARα pathways, suggesting impaired fasting adaptation and reduced hepatic catabolic capacity. Collectively, these findings demonstrate that paternal nicotine exposure induces sex-dependent metabolic reprogramming, with pronounced effects on glucose homeostasis in females and transcriptional signatures of reduced fasting resilience in males. These results identify the liver and adipose tissue as key targets of paternal nicotine exposure in the offspring and underscore the need for longitudinal studies to determine whether these alterations predispose offspring to metabolic disease across the lifespan

overall_design: 3' tag RNA seq profiling for liver and gonadal white adipose tissue in C57BL/6J males and females patternally exposed to nicotine and control

first: Stephanie

last: Aguiar

first: Truman

last: Natividad

first: Daniel

last: Davis

first: Carlos

last: Diaz-Castillo


title: Ion Torrent RNA-sequencing of microdissected chemorefractory and chemosensitive high-grade serous ovarian cancer samples

city: Houston

first: Chi Lam

last: Au Yeung

state: TX

address: 1515 Holcombe Blvd

institute: The University of Texas MD Anderson Cancer Center

type: Non-coding RNA profiling by high throughput sequencing

summary: To identify miRNAs that are associated with intrinsic chemoresistance, we performed next-generation Ion Torrent miRNA-sequencing analysis on RNA isolated from microdissected chemo-refractory samples (i.e., tumors not responsive to initial chemotherapy) and microdissected chemo-sensitive samples (i.e., tumors with relapsed HGSC 6 months after the last cycle of chemotherapy) of treatment-naïve advanced high-grade serous ovarian cancer (HGSC). We identified an miRNA signature with a set of miRNAs and their variants that showed significant differential copy numbers in chemo-refractory samples compared to chemo-sensitive samples.

overall_design: Samples are RNA extracted from microdissected chemo-refractory and chemo-sensitive samples of treatment-naïve advanced high-grade serous ovarian cancer.

first: Chi-Lam

last: Au-Yeung

first: Tetsushi

last: Tsuruga

first: Kwong-Kwok

last: Wong


title: Oncogenic and tumor-suppressive forces converge on a progenitor-orchestrated niche to shape early tumorigenesis [KPLOH scRNA-seq]

first: Yu-Jui

last: Ho

state: New York

overall_design: To study the consequences of p53 loss of heterozygosity during pancreatic cancer initiation, we conducted single cell RNA sequencing on dissociated epithelial cells derived from the KPLOH mouse model. In this system, Kras-mutant epithelial cells that retain wild-type p53 are mKate2/GFP double-positive, whereas cells undergoing spontaneous p53 LOH become mKate2 single-positive due to co-deletion of a physically linked GFP reporter. We isolated collected mKate2+/GFP+ and mKate2+/GFP- cells from mice that did not have a macroscopic tumor mass (pretumor stage), and from mice that had macroscopic PDAC (tumor stage).

first: José

last: Reyes

first: Scott

last: Lowe

first: Dana

last: Pe'er


title: Xing-Pi-Qing-Gan decoction alleviates alcoholic liver disease through multi-omics and experimental verification of DDIT3-Nrf2/HO-1-mediated antioxidant defense

city: Hangzhou

first: Nafei

last: Huang

address: The Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, People’s Republic of China

summary: This study aimed to investigate the transcriptome changes of alcoholic liver disease treated with NIAAA model after administration of Xing-Pi-Qing-Gan decoction. The mice were divided into two groups: one group of NIAAA model mice, and the other group was administered simultaneously on the basis of modeling. After the experiment, total RNA was extracted from fresh liver for high-throughput RNA sequencing (RNA-seq), and the effect of Xing-Pi-Qing-Gan decoction on alcoholic liver disease and related host transcriptional changes were identified by differential gene expression analysis.

overall_design: A total of 8 RNA-seq samples were analyzed, including mouse liver tissue treated with the NIAAA model and mouse liver tissue administered Xing-Pi-Qing-Gan decoction simultaneously on the basis of the model, each containing four biological replicates.

first: Ping

last: Ling

first: Yujie

last: Xu

first: Xiaofeng

last: Feng

first: Yi

last: Zheng

first: Tao

last: Sun


title: Inhibition of p38 MAPK after repetitive mild TBI ameliorates immune signaling and behavioral deficit

city: Atlanta

first: Levi

middle: B.

last: Wood

state: GA

address: 315 Ferst Dr NW Rm 3303

institute: Georgia Institute of Technology

summary: Background: Mild head injury associated with long-term functional impairments (i.e., depression, anxiety) is frequently observed among patients who experienced mild traumatic brain injury (mTBI). Moreover, repetitive injuries within a window of vulnerability can lead to exacerbated consequences compared to a single mTBI. However, current interventions for mTBI focus on alleviating symptoms, rather than targeting underlying mechanisms. Following the initial mechanical impact, increasing evidence suggests that the brain undergoes an inflammatory cascade consisting of pro-inflammatory intracellular signaling pathways and production of cytokines, ultimately leading to chronic neuroinflammation and persistent neurological deficits, such as depression. Specifically, in the context of severe brain injury, the p38 MAPK signaling pathway has been identified as a key driver to the inflammatory response, associated with increased microglial activation, proinflammatory cytokines, and synaptic dysfunctions, but its role in the context of mild brain injury remains unclear.  As such, this study aimed to investigate whether p38 MAPK drives the inflammatory responses and longer-term deficits following a weight-drop mouse model of repetitive mTBI (rmTBI). Methods: We injected C57/BL6 mice with SB239063, a small molecule p38 MAPK inhibitor, after each of the 5 once-daily weight-drop closed head injuries (CHIs) or sham. We evaluated functional outcomes within 4-weeks after the final CHI and quantified cytokine expressions, microglia reactivity, and transcriptional profiles at 4hr and 4-weeks post final injury. Results:  We found that in females, acute inhibition of p38 MAPK attenuated acute inflammatory response comprised of increased cytokine/chemokine expression and microglial activation at 4-hours post injury and longer-term anti-depressive-like behavioral at 4-weeks post injury. However, such effects of p38 inhibition were less obvious in males. On the transcript level, we found that p38 inhibition not only normalized the effects of the brain injury but also upregulated protective genes and pathways associated with recovery and the maintenance of brain homeostasis. Together, these findings support the therapeutic potential of p38 MAPK inhibition following (r)mTBI, indicating the role of p38 MAPK in driving the acute and longer-term consequences post brain injury in a sex dependent manner.

overall_design: Mice aged to 2-4 months were randomly assigned to one of the two groups: five once-daily closed head injuries (5xCHI) or five once-daily sham injuries. Within each group, mice were then randomly assigned treatment or vehicle groups. The treatment group was given the p38 MAPK small molecule inhibitor SB239063 (SB) intraperitoneally (20 mg/kg in physiological saline); the vehicle group was given physiological saline. Treatment/vehicle was injected 30 minutes after each CHI or sham injury. We had a total of 4 experimental groups: 5xCHI + vehicle, 5xCHI + SB, sham + vehicle, sham + SB. Animals were sacrificed by cervical dislocation under 5% isoflurane (1L/min, 100% oxygen) at either a short or long time point. The short time point (acute) was 4h after the final CHI, and the long time point (chronic) was ~1 month after the final CHI (~18 and 34 days).

first: Chenxing

last: Li

first: Sydney

last: Triplett

first: Martin

last: Griffin

first: Anna

last: Silverio

first: Elizabeth

last: Pettit

first: Erin

last: Buckley


title: DPP4 inhibition affects metabolism and inflammation associated pathways in hiPSC-derived steatotic HLCs

city: Düsseldorf

first: Wasco

last: Wruck

address: Moorenstr. 5

institute: Universitätsklinikum Düsseldorf

summary: Background Metabolic dysfunction-associated steatotic liver disease (MAFLD) has a high prevalence and high co-morbidity for other diseases. Due to the complexity of this multifactorial disease, therapy options are still rather limited. We employed an in vitro pluripotent stem cell-based model to decipher potential disease-associated molecular pathways and to study the mode of action of prospective drugs. Dipeptidyl peptidase 4 (DPP4) or Cluster of differentiation 26 (CD26) is involved in inflammation, infections, immune disorders, type 2 diabetes, kidney disease and cancer.  Methods We induced the steatosis phenotype in human induced pluripotent stem cell (iPSC) derived hepatocyte-like cells (HLCs) by oleic acid (OA)-feeding and confirmed regulation of clinically relevant pathways by NGS-based global transcriptomic analyses. Analysis of the secretome of steatotic HLCs revealed DPP4 as a potential key mediator of the disease. To further elucidate its role in the development of MAFLD, we inhibited DPP4 activity with Vildagliptin (VILDA) and analyzed the global transcriptome changes as well as specific gene and protein expression of steatosis-associated genes with and without DPP4 inhibition.  Results MAFLD-associated pathways such as PPAR- and TNF signaling were differentially regulated in hiPSC-derived steatotic HLCs. We found increased hepatic DPP4 activity and secretion upon OA. Gene expression of fatty acid and purine metabolism and inflammation-associated pathways were regulated upon DPP4 inhibition.  Conclusions Our HLC-model confirmed association of DPP4 with metabolism and inflammation which foster the development of MAFLD. Inhibiting DPP4 with VILDA partially relieved the steatotic phenotype on a global transcriptomic level.  Impact and implications Given the difficulties of identifying suitable anti-MAFLD drugs, novel model systems are urgently needed. Our in vitro HLC-model reproduced DPP4-dependent aspects of the disease and responded positively to Vildagliptin treatment. Further elucidation of the role of DPP4 in the etiology of MAFLD and other diseases is warranted.

overall_design:
hepatocyte-like cells derived from induced pluripotent stem cells of control and steatosis patients with and witout oleic acid treatment were compared

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

first: Christiane

last: Lörch

first: Julian

last: Reiss

first: James

last: Adjaye

first: Nina

last: Graffmann


title: DPP4 inhibition affects metabolism and inflammation associated pathways in hiPSC-derived steatotic HLCs [Vilda]

overall_design:
hepatocyte-like cells derived from induced pluripotent stem cells with and witout oleic acid and Vildagliptin treatment were compared

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


title: Nucleosome spacing regulates linker methylation by DNMT3A2/3B3

city: Grand Rapids

first: Peter

last: Jones

state: MI

address: 333 Bostwick Ave NE

department: Center of Epigenetics

institute: Van Andel Research Institute

type: Methylation profiling by high throughput sequencing

summary: CpG methylation (mCpG) is essential for mammalian development and is deposited by the de novo DNA methyltransferases DNMT3A and DNMT3B, which preferentially target DNA linkers between nucleosomes. Although cells contain millions of unique linkers, the rules that dictate which linkers get targeted by DNMT3 enzymes are not understood. Here, we show that nucleosome spacing governs linker DNA methylation and H3K36me2 recognition by the DNMT3A2/3B3 tetramer, directly linking de novo methylation to chromatin structure and nucleosome remodeling. We present the first structures of DNMT3A2/3B3 bound to di-nucleosomes, revealing inter-nucleosome interactions that control methylation. DNMT3A2/3B3 bridges nucleosomes separated by short DNA linkers, suppressing methylation, while long linkers allow DNMT3A2/3B3 to engage each nucleosome separately, promoting methylation. Finally, DNMT3A2/3B3 scans for properly modified substrates by positioning its PWWP domain at the H3 tail exit site, however H3K36me2 recognition is blocked when DNMT3A2/3B3 bridges di-nucleosomes with short linkers. Together, these findings uncover the mechanisms that govern de novo methylation in chromatin and explain how DNMT3 enzymes target specific linkers in living cells.

overall_design: To systematically dissect effects of linker length on CpG methylation by 3A2/3B3, we reconstituted a set of di-nucleosome substrates with 38bp and 40bp overhangs (comprising a 10bp overhang sequence with 28bp or 30bp sequencing primer binding sites) and linker DNA lengths ranging from 5bp-35bp (Fig. 1a). We hereafter refer to these as Y-X-Y di-nucleosomes, where Y indicates the overhang length and X indicates the linker length. We inserted specific CpG dinucleotides in the linker DNA, then incubated the di-nucleosomes with 3A2/3B3 and the SAM methyl donor to allow linker methylation. After the reaction, we collected endpoints to simultaneously assess the effects of linker length and CpG location on DNA methylation using bisulfite sequencing.

first: Minmin

last: Liu

first: Xiaoyan

last: Xie

last: A. Jones

first: Evan

last: J. Worden


title: Integrated Multi-omics Profiling of Mouse Brain Tissue Using the AllPrep Methods versus Traditional Extraction Methods

city: Tianjin

first: Bingqian

last: Chu

address: Cell and Organism Ecological Laboratory, Yuexin Dao, Haihe River

institute: Chinese Academy of Medical Sciences & Peking Union Medical College

summary: This study systematically evaluated the AllPrep co-extraction strategy in multi-omics analysis of mouse brain tissues. At the transcriptomic level, AllPrep produced higher RNA yields and an 88.14% gene detection rate, ensuring broader coverage. In proteomics, it preserved identification depth while improving detection of membrane proteins, ubiquitin ligases, and transcription factors. Phosphoproteomics further revealed 4,347 high-confidence phosphorylation sites, including CAMK family regulatory patterns. Integrated analysis showed stronger RNA–protein correlations and enriched neuroscience-related pathways. Overall, AllPrep provides a standardized, scalable workflow that enhances data quality and supports deeper exploration of neurobiological mechanisms.

overall_design: The mouse brain tissues were subjected to parallel multi-omics analysis through two extraction protocols: (1) conventional methods and (2) commercial kit-based approaches for RNA and protein extraction, followed by phosphoprotein enrichment.

first: Xianfeng

last: Shao


title: Expression Data from bone marrow derived macrophages derived from wildtype and STAT6(-/-) mice after stimulation (non-stimulation) for 24 hours with IL4/IL13.

city: Greifswald

first: Sabine

last: Ameling

address: Felix-Hausdorff.Str 8

department: Interfakultäres Institut für Genetik und Funktionelle Genomforschung

institute: Universitätsmedizin Greifswald

summary: Bone marrow derived macrophages from wild type and STAT6(-/-) mice after 24 hours stimulation using IL4/IL13 (10ng/mL) (in replicates N = 3 per group). Cells without stimulation refer as controls.

overall_design: We used microarrays to investigate the bone marrow derived macrophages from wild type and STAT6(-/-) mice after stimulation using IL4/IL13 (10ng/mL)

first: Matthias

last: Sendler


title: Systematic Transcriptome Analysis Reveals the Crucial Role of Alternative Promoters in Hematopoietic Lineages

first: Zhang

last: Tianzhe

address: Donghu Road 116, District Wuchang

department: Medical Research Institute

institute: Wuhan University

summary: Alternative promoters generate transcript isoforms with distinct exon compositions, playing critical roles in the precise regulation of lineage-specific gene expression. Yet it is largely unknown about their usage and functional relevance during hematopoietic development. In this study, we performed a comprehensive transcriptomic analysis of 532 RNA-seq datasets spanning 57 hematopoietic cell types and constructed a high-resolution landscape of alternative promoter activity. Among 1,074 high-impact promoters, Pou2f1 and Ikzf1 were identified as novel examples of lineage-associated alternative promoter usage. Ikzf1 P1 was predominantly active in B cells and monocytes, whereas Ikzf1 P2 exhibited selective activity in T cells. Pou2f1 P1 was active in T cells, NK cells and Monocytes, whereas Pou2f1 P2 was largely restricted to B cells. To assess functional relevance, we employed CRISPRi technology with sequence-specific sgRNAs to repress individual promoters and validate their lineage-specific contributions. Further, we identified the upstream regulatory factors that drive alternative promoter activation: Spi1 for Ikzf1 P1, Foxo1 for Ikzf1 P2, YY1 for Pou2f1 P1 and Pax5 for Pou2f1 P2. Therefore, our findings provide novel insights into the functional landscape of alternative promoters in hematopoiesis, as well as establish a foundation for future therapeutic interventions targeting promoter-specific regulation in hematopoietic-related disorders.

overall_design: CRISPRi  expriments in T cells and B cells, for T cells Pou2f1 P1 promoter was repressed when compared to Mock and for B cells, Pou2f1 P1 P2 promoters were repressed by sgRNA-1 and sg RNA-2.


title: Consistent lack of efficacy of nintedanib in a spirometry-confirmed and bleomycin-induced mouse model of idiopathic pulmonary fibrosis

city: Hørsholm

first: Henrik

last: Hansen

address: Hørsholm Kongevej 11

department: Histology & NGS

institute: Gubra

summary: Nintedanib, a multitargeted tyrosine kinase inhibitor, is approved for idiopathic pulmonary fibrosis (IPF) for its ability to slow lung function decline. This study systematically evaluated the effects of nintedanib across three independent treatment intervention studies in the single-dose bleomycin (BLEO) mouse model of IPF. In each study, male C57BL/6J mice received a single intratracheal instillation of BLEO (n=15-18 per study) or saline (n=10 per study) and were randomized and stratified to treatment according to body weight and non-invasive whole-body plethysmography measured seven days after BLEO administration. BLEO-IPF mice were administered (PO, BID) vehicle, nintedanib (50 or 60 mg/kg), or an activin receptor-like kinase 5 inhibitor (ALK5i, SB525334, 60 mg/kg) for up to 21 days. In all studies, nintedanib consistently failed to improve lung health, as evaluated by lung function tests, biochemistry, histology and RNA sequencing. Plasma concentrations of nintedanib showed no correlation to any efficacy endpoint applied. Lung transcriptome signatures in nintedanib-treated BLEO-mice indicated upregulated mRNA expression of p-glycoprotein (P-gp), a known nintedanib efflux transporter, suggesting limited lung bioavailability of nintedanib in the model. In comparison, ALK5i significantly improved lung function and exhibited robust anti-fibrotic efficacy in the model. Collectively, these findings challenge the use of nintedanib as a benchmarking drug in the BLEO-IPF model.

overall_design: RNA-seq profiling of the inferior lobe samples from CTRL vehicle, nintedanib-treated BLEO-IPF, and BLEO-IPF vehicle mice.

first: Grzegorz

last: Maciag

first: Jamal

last: Bousamaki

last: Björk Hansen