title: A parabrachial hub for the prioritization of survival behavior during pain

city: Philadelphia

first: John

middle: Nicholas

last: Betley

state: Pennsylvania

address: 433 S University Avenue, Lynch Bldg, Rm 321

department: Biology

institute: University of Pennsylvania

summary: Long-term sustained pain following acute physical injury is a prominent feature of chronic pain conditions. Populations of neurons that rapidly respond to noxious stimuli or tissue damage have been identified in the spinal cord and several nuclei in the brain. Understanding the central mechanisms that signal ongoing sustained pain, including after tissue healing, remains a challenge. In this study, spatial transcriptomics, neural manipulations, activity recordings and computational modeling demonstrate that activity in an ensemble of anatomically and molecularly diverse parabrachial neurons that express the NPY Y1 receptor is elevated following injury and predicts functional coping behavior. Regardless of the injury type, hunger, thirst, or predator cues suppressed sustained pain by inhibiting PBN Y1R neurons via the release of NPY. Together, our results demonstrate an endogenous analgesic hub at pain-responsive parabrachial Y1R neurons

overall_design: To identify brain regions and cell types involved in persistent pain, we performed spatial transcriptomic profiling of the parabrachial nucleus (PBN) in mice following formalin-induced inflammatory injury. Mice were injected with 2% formalin into the dorsal hind paw, and brain tissue was collected one hour post-injection to capture ongoing pain-related gene expression. Coronal sections of the hindbrain encompassing the PBN were subjected to high-plex spatial transcriptomics using the NanoString CosMx platform. The goal was to identify molecularly and spatially defined populations of neurons activated during sustained pain, with a particular focus on NPY Y1 receptor-expressing (Y1R) neurons. Spatial and computational analyses were used to define transcriptomic clusters, assess activity-induced gene expression, and map neuronal subpopulations implicated in chronic pain processing.

first: Nitsan

last: Goldstein

first: Amadeus

last: Maes

first: Heather

middle: N

last: Allen

first: Tyler

last: Nelson

first: Kayla

last: Kruger

first: Nicholas

last: Smith

first: Albert

middle: T

last: Yeung

first: Morgan

last: Kindel

first: Jamie

last: Carty

first: Lavinia

last: Boccia

first: Niklas

last: Blank

first: Emily

last: Lo

first: Rachael

last: Villari

first: Ella

last: Cho

first: Erin

last: Marble

first: Michelle

last: Awh

first: Yasmina

last: Dumiaty

first: Melissa

last: Chee

first: Rajesh

last: Khanna

first: Christoph

last: Thaiss

first: Bradley

last: Taylor

first: Ann

last: Kennedy


title: Effects of high cholesterol diet on liver small RNA expression profile utilizing two different RNA-seq methods

status: Public on Jul 02 2025

city: Riverside

first: Xiuchun

last: Li

address: 900 University Avenue

country: USA

institute: UCR

type: Non-coding RNA profiling by high throughput sequencing

summary:
Purpose: To  reveal the small RNA profiles in the liver using traitional and PANDORA-seq methods
Methods: 8 week old C57BL/6 male mice were fed a high cholesterol or low cholesterol diet for 4 weeks. Liver RNA was extracted by injecting Trizol into the aorta and collecting the flow through for further processing
Results: PANDORA-seq revealed an abundant amount of tsRNA and rsRNA that were undetected by traditional-seq. Importantly, PANDORA-seq revealed that many differentially regulated sncRNAs also undetected with traditional-seq

overall_design: Liver small RNA were sequenced from C57BL/6 male mice after 4 weeks of low cholesterol or high cholesterol feeding

first: Tong

last: Zhou

first: Changcheng


title: Identification of Neuritin 1 as a local metabolic regulator of brown adipose tissue.

status: Public on Jul 04 2025

city: Barcelona

first: Camille

last: Stephan Otto Attolini

state: Select a State or Province

address: Baldiri Reixac 10

department: Biostatistics and bioinformatics Unit

country: Spain

institute: IRB Barcelona

type: Expression profiling by high throughput sequencing

summary: Brown adipose tissue (BAT) plays a key role in metabolic homeostasis through its thermogenic effects and the secretion of regulatory molecules. Here we report that RAP250 haploinsufficiency stimulates BAT in mice, thus contributing to a decrease in fat accumulation. Local in vivo AAV-mediated RAP250 silencing in BAT reduces body weight and fat mass and enhances glucose oxidation, thereby indicating that RAP250 participates in the regulation of BAT metabolic activity.   Analysis of the mechanisms  led to the finding that Neuritin 1 is produced and released by brown adipocytes, it plays a key metabolic role, and it participates in the enhanced BAT metabolic activity under RAP250 deficiency.  Forced overexpression of Neuritin 1 in UCP1-expressing cells markedly decreases fat mass and body weight gain in mice and induces the expression of thermogenic genes in BAT. Neuritin 1-deficient brown adipocytes also shows a reduced b-adrenergic response. We demonstrate a metabolic role of BAT-derived Neuritin 1 acting through an autocrine/paracrine mechanism.  Based on our results, Neuritin-1 emerges as a potential target for the treatment of metabolic disorders.

overall_design: RNA-seq profiling of Intescapular brown adipose tissue of WT and RAP250 heterozygous 20 week-old male mice

first: Manuela

last: Sánchez-Feutrie

first: Montserrat

last: Romero

first: Antonio

last: Zorzano

first: Vanessa

last: Hernández

first: Óscar

last: Reina


title: Using human urinary-derived renal epithelial cells for deep phenotyping of NPHP1 deletion and determining personalised response to novel therapeutics

status: Public on Jul 01 2025

city: Newcastle Upon Tyne

first: Juliana

middle: Estefania

last: Arcila-Galvis

state: Selecciona un estado

address: 258A  BAxterwood Court, Newcastle Upon Tyne, Tyne and Wear, NE4 5HW

department: Biosciences Institute

country: United Kingdom

institute: Newcastle University

summary: Nephronophthisis (NPHP) is an autosomal recessive tubulointerstitial nephropathy classified as a renal ciliopathy disorder and recognised as the leading genetic cause of kidney failure in children and young adults. NPHP1 is the most common genetic cause and encodes nephrocystin-1, a protein that plays crucial roles in the primary cilium and cellular junctions. Here we utilise personalised medicine approaches and deep phenotyping, which enable us to explore mechanistic pathways and identify potential therapeutic strategies. In a family where we detected a homozygous NPHP1 whole-gene deletion in three affected siblings, we compared kidney biopsy tissue and human urine-derived renal epithelial cells (hURECs). Both the kidney biopsy and the hURECs demonstrated renal epithelial cells with an elongated and tortuous primary ciliary phenotype. Bulk RNA-seq on patient hURECs revealed disease signatures of the NPHP1 homozygous deletion, which included changes in EGFR signaling, as well as extracellular matrix interactions and adherens junctions, in line with the original description of nephrocystin-1 as an adapter protein at adherens junctions. Treatment of patient hURECs with alprostadil, a recently proposed therapy for NPHP, caused an increase in overall ciliation rate, but also an exaggerated primary ciliary length. In contrast, treatment of patient hURECs with an EGFR kinase inhibitor produced a phenotypic rescue of ciliary length and tortuosity. Following hUREC treatments, alprostadil did not fully restore the disease-associated transcriptional profile, whereas treatment with the EGFR kinase inhibitor AG556 caused a more complete rescue of the transcriptomic disease signature, in keeping with the observed phenotypic rescue. We conclude that patient-derived hURECS enable the deep phenotyping of nephronophthisis, replicate human kidney biopsy findings, and can be used to develop disease pathway signatures and screen candidate drug molecules, providing novel insights into disease pathogenesis and therapies. EGFR inhibition is now a potential therapy for renal ciliopathies, which should be tested within in vivo models of NPHP as a prelude to human studies.

overall_design: RNA-seq profiling was performed on primary urine-derived renal epithelial cells isolated from a male patient with nephronophthisis and an age- and sex-matched healthy control. The dataset includes sequencing of untreated cells, as well as cells treated with a PGE2 receptor agonist, DMSO as a vehicle control, or an EGFR kinase inhibitor.

first: Juliana E.

first: Praveen Dhondurao

last: Sudhindar

first: Marco

last: Trevisan-Herraz

first: John A

last: Sayer


title: Enhancing single-cell ATAC sequencing with formaldehyde fixation, cryopreservation, and multiplexing for flexible analysis [ATAC-seq]

city: Freiburg im Breisgau

first: Thomas

last: Manke

address: Stuebeweg 51

department: Bioinformatics Core Facility

country: Germany

institute: Max-Planck-Institute of Immunobiology and Epigenetics

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The assay for transposase-accessible chromatin using sequencing (ATAC-seq) revolutionized the field of epigenetics since its emergence by providing a means to uncover chromatin dynamics and other factors affecting gene expression. The development of single-cell (sc) applications in recent years led to an even deeper understanding of cell type specific gene regulatory mechanisms. One of the major challenges while running ATAC-seq experiments, bulk or sc, is the need for freshly collected cells for successful experiments. While various freezing methods have already been tested and established for bulk and sc ATAC-seq, quality metrics for preserved cells are rather poor or dependent on sampling time when compared to fresh samples. This makes it difficult to conduct all sorts of complex experiments i.e. with multiple conditions, patients, or time course studies. Especially, accounting for batch effects can be difficult if samples need to be processed at different time points of collection. We tackled this issue by adding a fixation step prior to the freezing method. The additional fixation step improved library quality and yield data comparable to fresh samples. The workflow was also tested on multiplexed sc ATAC experiments, set-up for cost-efficient low input sample handling. Sample cross-in, typically encountered in Tn5-based multiplex approaches, were tackled with a computational procedure specifically developed for this approach.

overall_design: To investigate the performance of our sample preservation and multiplexing strategies, we harvested cultured HepG2 cells. The cells were fixed with 0.1-5% Formaldehyde and subsequently frozen by either flash freezing or cryopreservation. Then, ATAC-seq libraries were created and sequenced to analyze the influence of each preservation combination on data quality and comparability.

first: Hohl

last: Tobias

first: Boenisch

last: Ulrike

first: Manke

last: Thomas

first: Arrigoni

last: Laura


title: Hijacking intrinsic resistance in Mycobacterium abscessus with small molecule prodrugs

city: Memphis

first: Richard

last: Lee

state: TN

address: 262 Danny Thomas Place

department: Department of Chemical Biology and Therapeutics

institute: St. Jude Children's Research Hospital

summary: This proposal aims to develop narrow-spectrum prodrug-activated protein synthesis inhibitors to treat Mycobacterium abscessus (Mabs) infections. It builds on a recent discovery in our program, which elucidated a unique mechanism for prodrug activation of florfenicol amine (FFA) by hijacking the protective methods Mabs uses to block antibiotic action. Non-tuberculous mycobacteria (NTM) are emerging pathogens with high intrinsic drug resistance.  Mabs is the most pathogenic refractory NTM member,1-3 and infections with this pathogen are associated with especially poor clinical outcomes, similar to XDR-TB (extensively drug-resistant tuberculosis)1.  Florfenicol (FF) is a broad-spectrum analog of chloramphenicol (CAM), is orally bioavailable, safely used in agriculture as it lacks some of the pharmacological liabilities of CAM, and it mitigates plasmid-borne resistance by blocking the primary-hydroxy site of inactivation. FFA is the primary metabolite found in many host species after FF administration. Through routine MIC screening of synthetic intermediates, we discovered that FFA on its own had appreciable WhiB7 transcription factor-dependent MIC activity against Mabs.  Further studies demonstrated that in Mabs FFA acts as a prodrug that is acylated into the active form (FFac) within Mabs by Eis2, a Mabs specific acetyltransferase. eis2 is located in the whiB7 resistome, which results in a feed-forward mechanism of action between FFA, eis2, and whiB7, ultimately increasing the conversion of FFA to FFac, resulting in increased sensitivity. FFA was found to be highly synergistic with other protein synthesis inhibitors and resistance to FFA by inactivation of whiB7 or eis2 results in increased sensitivity to aminoglycosides and macrolides. Since eis2 is only present in Mabs and other closely related species, FFA has a narrow spectrum of activity and avoids the potential for mitochondrial cytotoxicity. Preliminary pharmacological studies demonstrate FFA is noncytotoxic and orally bioavailable.

sample_organism:
Mycobacteroides abscessus
Mycobacteroides abscessus ATCC 19977

overall_design: mRNA profiles of Mycobacterium abscessus ATCC19977 strain after exposure to 1/2 minimal inhibitory concentration of chloramphenicol (256 mg/L) for 30 minutes, florfenicol and florfenicol amine at 25 µM for 30 minutes and 3 hours, and vehicle control at 30 minutes and 3 hours.

first: Gregory

middle: A

last: Phelps

middle: E


title: Quiescent fibroblast-like synovial cells alleviate inflammatory bowel disease by modulating the gut immune microenvironment [dataset 1]

city: Shijiazhuang

first: Jiayu

last: Zhang

address: No. 361 Zhongshan East Road

country: China

institute: Hebei Medical University

summary: To explore the potential of stem cellsfromhuman exfoliated deciduous teeth (SHED) for the treatment of inflammatory bowel disease (IBD) by addressing their in vivo mechanisms.

overall_design: scRNA-seq of Stem cells from Human Exfoliated Deciduous teeth (SHEDs) and intestinal organoid medium cultured-SHED (CM-SHEDs)


title: RNA-Seq sequencing of Aspergillus fumigatus strain CEA10 at 37°C and 42°C

city: Jena

first: Matthew

middle: George

last: Blango

address: Adolf-Reichwein-Str. 23

department: Junior Resaerch Group RNA Biology of Fungal Infections

institute: Leibniz Institute for Natural Product Research and Infection Biology

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

overall_design: Refer to individual Series


title: Effect of FL-Fc-DM1 drug on gene expression of MV-4-11 cells pretreated with cytarabine.

status: Public on Jun 30 2025

city: Shenzhen

first: Dengyang

state: Guangdong

address: Zhenmei road, guangming district

institute: Seventh affiliated hospital, Sun Yat-sen University

summary: Cytarabine is one of the first line chemo drugs to treat acute myeloid leukemia (AML). However, cytarabine can induce AML cell cell cycle arrest at G0/G1 phase. These cell-cycle-arrested AML cells resist cytarabine, show a senescence-like phenotype or stem-cell like phenotype. To eliminate these cell-cycle arrested cells, we developed a FL-Fc-DM1 drug by conjugating FLT3 liangd Fc fusion protein and mertansine. We used the MV-4-11 cells as a AML model. The total mRNA of MV-4-11 cells treated with different drugs (cytarabine, FL-Fc-DM1) were sequenced.

overall_design: MV-4-11 cells were cultured in IMDM medium supplemented with 10% FBS. In the control group, MV-4-11 cells were cultured for 4 days. In the cytarabine group, MV-4-11 cells were treated with 2/5 µM cytarabine for 4 days. In the FL-Fc-DM1 treatment group, MV-4-11 cells were treated by cytarabine (2/5 µM) for 3 days and then treated with FL-Fc-DM1 (1 nM) for another 24 hours in the absence of cytarabine. We than analyze the transcriptome differences between different groups.

first: Yun

last: Chen


title: Gene expression profile at single embryo level of 0-3h old hybrid Drosophila embryos

status: Public on Jul 03 2025

city: Grand Rapids

first: Adelheid

last: Lempradl

state: Michigan

address: 333 Bostwick Ave NE

department: Metabolism and Nutritional Programing

institute: Van Andel Institute

summary: We used single-embryo RNA-sequencing (RNA-seq) to characterize early zygotic gene expression in Drosophila. To assess the accurate transcriptional activation for zygotic genes, we analyze the paternal allele expression as embryos initially contain trace amounts of paternal mRNAs delivered by the sperm. For this purpose, we used two genetically different lines from the Drosophila Genetic Reference Panel (DGRP) with known genetic variations in our crosses (males/DGRP_352, females/DGRP_737). The data provide a continuous timeline of transcript levels and allele-specific gene expression during early development (≤ 3 hours) in Drosophila melanogaster. Deposited RNA-seq data is part of a multi-'omics approach and prior metabolite extraction was performed in each sample.

overall_design: RNA from single Drosophila embryos was isolated and used for library preparation by a modified CelSeq2 single-cell RNA-seq protocol. Next, we performed pseudo-temporal analysis on the single-embryo RNA-seq data to get a high-resolution, time-resolved picture of transcriptional events during early embryonic development. To get allele-specific gene expression, we performed variant calling on the hybrid offspring by a modified GATK’s workflow retaining only known and biallelic SNPs annotated to a single gene. Finally, we match our pseudo-time analysis with the allele-specific gene expression in each embryo. Note: the normalized reads in pseudo-time order that are provided as supplementary file include 8 unfertilized eggs (prefix U) which should be excluded when exclusively analyzing  embryo development (n=245 embryos, prefix E).

first: J

last: Perez-Mojica

first: Kin

middle: H

last: Lau


city: Lyon

first: Frédéric

last: Flamant

state: France

address: 46 allée d'Italie

department: IGFL

country: France

institute: ENSL

summary: We present a cheap, rapid, and versatile assay called SOSHI-seq (Screening Of Self-transcribed Hormone Inducible response elements coupled to sequencing). The protocol is an adaptation of the STARR-seq method, which allows testing the capacity of thousands of synthetic DNA sequences to act as hormone-response elements. Using the nuclear receptors of thyroid hormone as an example, we show that SOSHI-seq is a suitable complement to ChIP-Seq analysis to identify at genome-wide scale the functional response elements occupied by nuclear receptors in chromatin.

overall_design: SOSHI-seq: a high-throughput screening assay to test the functionality of putative response elements for nuclear hormone receptors. SOSHI-seq: a high-throughput screening assay to test the functionality of putative response elements for nuclear hormone receptors. Banks are prepared with 1000 inserts in a plasmid vector in which sequences able to bind a nuclear receptor are inserted. Plasmid banks are transfected in HEK293 cells and RNA is extracted. Amplicons are prepared, corresponding to the variable part of the plasmid transcript. Amplicons are used to prepare sequencing libraries. Samples differ by : - the plasmid bank that is transfected (bank1 or bank2) - the type of nuclear receptor that is encoded by an additionnal plasmid that is cotransfected with the bank (TRα1, TRβ1 or  LXRα) - the presence or absence of agonist in the culture medium (thyroid hormone , or T3, for TRα1, TRβ1, T-compound for  LXRα). Some of the experiments are duplicated.

first: Shijia

last: Wu

first: Romain

last: Guyot

first: Yanis

last: Zekri

first: Whenzeng

last: Jiang


title: Enhancing single-cell ATAC sequencing with formaldehyde fixation, cryopreservation, and multiplexing for flexible analysis [scATAC-seq]

first: Thomas

last: Manke

overall_design: To investigate the performance of our sample preservation and multiplexing strategies, we harvested cultured HepG2 cells. The cells were fixed with 0.1% FA and subsequently frozen by either flash freezing or cryopreservation. An untreated sample was also included. Then, scATAC-seq libraries were created and sequenced to analyze the influence of each preservation method on data quality and comparability.

first: Hohl

last: Tobias

first: Boenisch


title: Effect of FL-Fc-DM1 drug on gene expression of Molm-13 cells pretreated with cytarabine.

summary: Cytarabine is one of the first line chemo drugs to treat acute myeloid leukemia (AML). However, cytarabine can induce AML cell cell cycle arrest at G0/G1 phase. These cell-cycle-arrested AML cells resist cytarabine, show a senescence-like phenotype or stem-cell like phenotype. To eliminate these cell-cycle arrested cells, we developed a FL-Fc-DM1 drug by conjugating FLT3 liangd Fc fusion protein and mertansine. We used the Molm-13 cells as a AML model. The total mRNA of Molm-13 cells treated with different drugs (cytarabine, FL-Fc-DM1) were sequenced.

overall_design: Molm-13 cells were cultured in RPMI 1640 medium supplemented with 10% FBS. In the control group, Molm-13 cells were cultured for 4 days. In the cytarabine group, Molm-13 cells were treated with 0.5/1 µM cytarabine for 4 days. In the FL-Fc-DM1 treatment group, Molm-13 cells were treated by cytarabine (0.5/1 µM) for 3 days and then treated with FL-Fc-DM1 (1 nM) for another 24 hours in the absence of cytarabine. We than analyze the transcriptome differences between different groups.


title: CRISPR Screening Reveals a Novel Role for FOXH1 in Regulating Pluripotency of Porcine Embryonic Stem Cells

city: Wuhan

first: Wu

last: Linhui

state: Hubei

address: No.1 Shizishan Street

department: College of Animal Science and Veterinary Medicine

institute: Huazhong Agricultural University

summary: pESCs hold significant potential for applications in regenerative medicine and stem cell-based breeding programs. However, the regulatory mechanisms governing pluripotency in pESCs, including aspects of cellular adaptability and the maintenance of a pluripotent identity, are not yet fully understood.To distinguish these two features of pESCs, we conducted two types of CRISPR-Cas9 knockout screenings targeting all known transcription factors and epigenetic regulators in the porcine genome. Through the CRISPR-Cas9 screenings, we identified 900 essential genes, including the species-conserved gene PRMT1 and the pig-specific gene NASP, which were experimentally validated for their roles in preserving the survival of pESCs. In addition, we found that FOXH1 is indispensable for maintaining pESCs pluripotency. pESCs deficient in FOXH1 displayed a flatter and more dispersed clonal morphology, accompanied by downregulation of pluripotency genes and upregulation of lineage-specific genes. In parallel, FOXH1 knockdown significantly impaired blastocyst formation during early pig embryogenesis, demonstrating an unrecognized role of FOXH1 that is not conserved in hESCs. At the molecular level, FOXH1 exhibits a dual role by regulating chromatin accessibility at pluripotency gene loci and H3K4me3 modifications at the promoters of developmental genes. The resources developed through this study not only lay the groundwork for more extensive CRISPR screenings but also provide crucial theoretical support for the establishment of pPSC cell lines with higher differentiation potential.

overall_design: This study employs multiple high-throughput sequencing technologies, including NGS, ATAC-seq, ChIP-seq, and RNA-seq, to comprehensively investigate the dynamics of sgRNA loss or enrichment during the library screening process, and to assess the effects of FOXH1 knockout on chromatin accessibility, transcription factor binding, and gene expression in pEPSCs. The dataset comprises samples from cell mutation libraries across different generations and pEPSCs under a variety of conditions, such as wild-type and gene knockout (e.g., FOXH1).

first: Peng

last: Su

first: Linhui


title: Effect of FL-Fc-DM1 drug on gene expression of THP-1 cells

summary: To eliminate  cell-cycle arrested AML cells, we developed a FL-Fc-DM1 drug by conjugating FLT3 liangd Fc fusion protein and mertansine. We used the THP-1 cells as a AML model. The total mRNA of THP-1 cells treated with different concentration of FL-Fc-DM1 were sequenced.

overall_design: THP-1 cells were cultured in RPMI 1640 medium supplemented with 10% FBS. In the control group, THP-1 cells were cultured for 1 day. In the FL-Fc-DM1 treatment groups, THP-1 cells were treated with FL-Fc-DM1 (1 and 3 nM) for 24 hours. We than analyze the transcriptome differences between different groups.

last: zhang


title: Effect of FL-Fc-DM1 drug on gene expression of Molm-13 cells

summary: To eliminate  cell-cycle arrested AML cells, we developed a FL-Fc-DM1 drug by conjugating FLT3 liangd Fc fusion protein and mertansine. We used the Molm-13 cells as a AML model. The total mRNA of Molm-13 cells treated with different concentration of FL-Fc-DM1 were sequenced.

overall_design: Molm-13 cells were cultured in RPMI 1640 medium supplemented with 10% FBS. In the control group, Molm-13 cells were cultured for 1 day. In the FL-Fc-DM1 treatment groups, Molm-13 cells were treated with FL-Fc-DM1 (1 and 3 nM) for 24 hours. We than analyze the transcriptome differences between different groups.


title: Tumor-infiltrating natural killer cell profiling for therapeutic stratification in smokers with resectable non-small cell lung cancer

city: Houston

first: Sung Wook

last: Kang

state: TX

address: one plaza

department: Surgery

institute: Baylor college of medicine

summary: Objective: Neoadjuvant chemoimmunotherapy has improved outcomes in resectable non-small cell lung cancer (NSCLC), yet its real-world implementation is often challenged by surgical delays, cancellations, immune-related fibrosis, and increased postoperative complications. Smokers with NSCLC, despite being at higher risk for postoperative complications, have enhanced responses to neoadjuvant chemoimmunotherapy. This study aimed to identify smoking-associated immune cell determinants that could inform treatment strategies. Methods: Single-cell RNA sequencing was performed on 61 lung samples from non-smokers, smokers, and patients with chronic obstructive pulmonary disease (COPD), as well as 8 invasive lung adenocarcinomas, to define smoking-related immune signatures. Using RNA sequencing data from 102 resected NSCLC and 24 NSCLC patients treated with neoadjuvant chemoimmunotherapy, we conducted in silico deconvolution to evaluate associations between cellular composition and clinical outcomes. Results: Among 140 lung cellular phenotypes, two natural killer (NK) cell subsets were strongly associated with smoking and COPD severity. “Stress-responsive NK (NKSR)” cells exhibited immature features and cytokine-responsive signatures. “Exhausted NK (NKExh)” cells showed mature features and elevated multiple immune checkpoint expression (PDCD1, TIGIT, and LAG3). Abundant intratumoral NKSR cells were associated with significantly improved survival after surgery, particularly in current smokers. Conversely, tumors with low NKSR and high NKExh cell profiles were associated with better responses to neoadjuvant chemoimmunotherapy. Conclusions: Tumor-infiltrating NK cell phenotyping may aid in therapeutic stratification in smokers with NSCLC. NKSR cell preservation predicts favorable outcomes with upfront surgery, while NKExh cell enrichment indicates greater benefit from neoadjuvant chemoimmunotherapy. These profiles may help optimize treatment by balancing therapeutic benefit and risk.

overall_design: This study was conducted under protocols approved by the Institutional Review Board at Baylor College of Medicine (BCM) (H-35782) and the University of Arizona (UA) (1811124026). Written informed consent was obtained from all participants for the collection of clinical data and biospecimens. At BCM, a prospectively maintained, single-institution database was reviewed retrospectively. The BCM cohort included 102 patients with histologically confirmed NSCLC who underwent complete pulmonary resection and mediastinal lymph node dissection. Staging was determined according to the 8th edition of the TNM classification. At UA (by Dr. Polverino), lung tissue samples were obtained from patients undergoing lung volume reduction surgery or lung transplantation for severe emphysema, or from patients undergoing lung resection for a solitary peripheral nodule, with sampled tissue taken from a region at least 10 cm away from the nodule. The UA cohort included 13 non-smokers, 21 ever-smoker control subjects, 15 patients with mild chronic obstructive pulmonary disease (COPD)(GOLD stage 1-2), and 12 patients with severe COPD (GOLD stage 3-4). COPD was defined as pre-bronchodilator forced expiratory volume in 1 second (FEV1)/forced vital capacity (FVC) ratio of less than 0.7 (70%). Disease severity was classified according to the GOLD criteria as follows: GOLD 1 (FEV1 ≥ 80%), GOLD 2 (50% ≤ FEV1 < 80%), GOLD 3 (30% ≤ FEV1 < 50%), and GOLD 4 (FEV1 < 30%).

first: Hyun-sung

last: Lee


title: Genome-wide binding of tomato AP1/FUL-like proteins determined by DNA-affinity purification sequencing (DAP-seq)

city: Wageningen

first: Xiaobing

address: Droevendaalsesteeg 1

department: Bioscience

country: Netherlands

institute: Wageningen University

summary: By function dissection in planta, we identified that tomato AP1/FUL-like genes have overlapping and specific functions in flowering and inflorescece development. In this experiment, we aim to identify the binding sites of AP1/FUL-like complexes (FUL2-J, FUL2-J2, FUL2-TM3, MC-J, MC-J2, MC-TM3) and determine if they exhibit binding to different targets or with differing affinities, which could be a mechanism to acquire target gene specificity. Specifically, we investigated this phenomenon for all the tetramers, as they are enriched in shoot reproductive meristems to fulfil the functions. Using the DAP-seq protocol, we established their genome-wide binding profiles and included input as control.

overall_design: We use DAP-seq to determine the genome-wide binding patterns of AP1/FUL-like protein FUL2 and MC with their interactors J, J2, and TM3 (FUL2-J, FUL2-J2, FUL2-TM3, MC-J, MC-J2, MC-TM3).

first: Kai

last: Thoris

first: Marian

last: Bemer


title: RNA sequencing of C elegans exposed to natural polyphenols

city: Frederiksberg C

first: Andrew

last: Williams

address: Dyrlægevej 100

country: Denmark

institute: University of Copenhagen

summary: C elegans worms were exposed to either honokiol or magnolol and global transcriptomic profiles determied to eludicate potential modes of action

overall_design: Nematodes were exposed to 200 uM of each compound for one hour prior to RNA extraction. Magnolol (plus DMSO control) were treated in triplicate, and honokiol in duplicate

middle: R


title: Effect of FL-Fc-DM1 drug on gene expression of MV-4-11 cells.

first: Dengyang

last: Zhang

summary: To eliminate  cell-cycle arrested AML cells, we developed a FL-Fc-DM1 drug by conjugating FLT3 liangd Fc fusion protein and mertansine. We used the MV-4-11 cells as a AML model. The total mRNA of MV-4-11 cells treated with different concentration of FL-Fc-DM1 were sequenced.

overall_design: MV-4-11 cells were cultured in IMDM medium supplemented with 10% FBS. In the control group, MV-4-11 cells were cultured for 1 day. In the FL-Fc-DM1 treatment groups, MV-4-11 cells were treated with FL-Fc-DM1 (0.5 and 1.5 nM) for 1 day. We than analyze the transcriptome differences between different groups.

first: Yun

last: Chen


title: Culture Media Strongly Influences Primary Human Bronchial Epithelial Cells' Transcriptomic Response to Ozone Exposure

city: Chapel Hill

first: Sarah

last: Lester

state: North Carolina

address: 120 Mason Farm Rd

department: Department of Genetics

institute: University of North Carolina at Chapel Hill

summary: Exposure to the ambient air pollutant ozone induces acute and chronic respiratory health effects in part by causing inflammation of the airways. Several aspects of the inflammatory response to ozone can be modeled in vitro using primary human bronchial epithelial cells (HBECs) cultured at an air-liquid interface. We tested two commonly used HBEC culture media systems, one proprietary and one non-proprietary, to identify which system yielded the most in vivo-like pro-inflammatory response to acute ozone exposure as indicated by gene expression. Cells from six donors were grown in each culture system in parallel followed by examination of epithelial morphology and cell type proportions prior to ozone exposure. Cultures grown in the proprietary system were notably thicker and contained more ciliated and secretory cells, as well as internal cyst-like structures. The transcriptomic response to acute ozone exposure (0.5 parts per million ozone x 2 hours) was strongly affected by media. HBECs grown in the proprietary system exhibited minimal changes after ozone, with only  only 7 differentially expressed genes (DEGs). In contrast,  HBECs grown in the non-proprietary system exhibited a more dynamic response with 128 DEGs, including hallmark response genes indicative of inflammation (CXCL8) and oxidative stress (HMOX1). Gene set enrichment analysis using the 128 DEGs further corroborated upregulation of oxidative stress and inflammation pathways. In total, our results indicate that the choice of HBEC culture media should be carefully considered to best model the in vivo response to ozone.

overall_design: RNA-seq profiling of well-differentiated primary human bronchial epithelial cells grown in PneumaCult or UNC media systems, collected 2hr after ozone or filtered air exposure.

first: Sabri

last: Abdelwahab

first: Scott

last: Randell

first: Samir

last: Kelada


title: EMT-ciliary signaling in quasi-mesenchymal-stem-like cells drives therapeutic resistance and is a druggable vulnerability in triple-negative breast cancer

city: Nantes

first: jennifer

last: Derrien

address: 8 quai moncousu

institute: INSERM

summary: Cancer therapeutic resistance is mediated, in part, by phenotypic heterogeneity and the plasticity of tumor cells, the latter being enabled by Epithelial-Mesenchymal Transition (EMT). However, EMT in human cancer therapeutic response remain poorly understood. We developed patient-derived organoids (PDOs) from human triple-negative breast cancer (TNBC) and investigated their response to chemotherapy. We found that chemotherapy treatment kills the bulk of tumor cells in PDOs, but there is selective survival of malignant cells that had activated an EMT program, entered a quasi-mesenchymal, stem cell-like state and display primary cilia. We developed a family of small-molecule inhibitors of ciliogenesis and show that treatment with these inhibitors, or genetic ablation of primary cilia, is sufficient to suppress this chemoresistance via NFB-induced cell death. We conclude that an EMT-ciliary signaling axis induces chemoresistance in quasi-mesenchymal stem-like cells to help tumors evade chemotherapy and represents a druggable vulnerability in human TNBC.

overall_design: Cancer cells dissociated from tumor tissue samples were used to generate PDOs. PDOs were dissociated and cells were processed for scRNAseq. PDOs from two different patient samples were used in the study. Non-treated PDOs were analyzed. Additionally, PDOs treated with DMSO (control: CTL) or doxorubicin or taxol or Nao-3 were used in the study.

first: Vincent J.

last: Guen

first: Jennifer


title: Epigenetically mediated drug resistance in myeloma is coordinated by a myeloma-associated long non-coding RNA PLUM [ChIP]

city: Singapore

first: Yinghui

last: Li

state: Singapore

address: 60 Nanyang Drive

department: School of Biological Sciences

country: Singapore

institute: Nanyang Technological University

summary: Multiple myeloma (MM) is the second most prevalent hematological malignancy that carries a poor prognosis. Despite significant advances in new treatments, most patients relapse due to the high genetic heterogeneity leading to treatment resistance. Recurrent mutations causing hyperactivation of the non-canonical NF-ĸB pathway are frequently enriched in relapsed, refractory MM patients, contributing to disease severity and drug resistance. Here, to identify NF-ĸB targets involved in chemoresistance, we combined multi-modal analysis of the NF-ĸB/p52 regulated myeloma epigenome with patient transcriptomics and uncovered a long non-coding RNA (lncRNA) linked to treatment resistant MM patients. The lncRNA termed PLUM is overexpressed in NF-ĸB+ high-risk MM subtypes and patients who are refractory to VRd (Bortezomib-Lenalidomide-Dexamethasone) treatment regimen. We reveal that PLUM interacts with Polycomb repressive complex 2 (PRC2) to regulate its stability and histone methyltransferase activity. Notably, PLUM binds to the disordered region of PRC2 subunit EZH2, modulating the expression of tumor suppressor genes, FOXO3 and ZFP36, to activate the unfolded protein response (UPR). Disruption of PLUM-EZH2 interaction using steric antisense oligonucleotides re-sensitized myeloma tumor cells to drug treatment, correlating with the loss of PRC2 stability and EZH2 H3K27 trimethylation activity. These findings indicate NF-ĸB/p52 regulated lncRNA, PLUM, modulates the myeloma epigenome by facilitating formation of PRC2 complex and EZH2 activity to mediate chemoresistance. Targeting specific PLUM-EZH2 interactions may represent a clinically important strategy for the treatment of relapsed, refractory MM.

overall_design: KMS-11 PLUM knock-down followed by RNA-seq (control/treated triplicates), H3K27me3 ChIP-seq (control/treated triplicates) and EZH2 ChIP-seq (endogenous triplicates)

first: Kamalakshi

last: Deka

first: Jean-Michel

last: Carter

first: Daniel

last: Ang

first: Akash

last: Bahai

first: Nicholas

last: Sim

first: Hooi

middle: Y

last: Chong

first: Guan

first: Suet

middle: M

last: Tan

first: Wee

middle: J

last: Chng

first: Dennis

last: Kappei


title: Serotonin through serotonylation impact on gene expresion on human purified trophoblast after 48h in culture

city: New Haven

first: Nolwenn

middle: Sue

last: Morris

address: 333 Cedar Street

department: OBGYN

institute: Yale University

summary: Serotonin (5-hydroxytryptamine) plays a critical role in human development in utero. Recent evidence suggests that it is taken up from the maternal circulation and gets concentrated in trophoblasts (Kliman et al., 2018). A novel mechanism involving serotonin has been described: serotonylation, a covalent linkage of 5-HT with protein glutamines mediated by a tissue transglutaminase (Farelly et al., 2019). Our objective was to understand the role of serotonin, through serotonylation, in protein, gene and phenotype expression in human placenta. Trophoblast puriScation and culture, western blot (WB), immunochemistry (IHC), and RNAseq (with IPA) were performed. Experiments were repeated at least 3 times, and corresponding statistical analysis was done. Through WB and IHC, we found that serotonylation seems to be present in human placenta and cytotrophoblasts. Moreover, through IHC and RNAseq/IPA, serotonylation seems to have consequences on gene and phenotype expression; especially on fusion, proliferation and invasion, which leads to implantation and placental structure, initial steps of pregnancy. Through IPA analysis, those phenotype and serotonylation impacted-genes were also found to be involved in embryonic, organismal, tissue and organ development, and especially the brain and behavior, foreshadowing central role in human body physiological development. Lastly, IPA results also showed that those same genes were also involved in many different pathologies, especially ones like Alzheimer, Parkinson, ALS, depression, ASD or cancer (EMT). To conclude, these Sndings seem to show that the human placenta, through the cytotrophoblast, is an essential organ to understand the origin of human life and pathophysiological development. Serotonin, through serotonylation, seems to be central by regulating original embryonic genes involved in different processes during life, especially in initiation of pregnancy (invasion and placentation), development of the human body, behavior, and different pathologies, leading to potential diagnostic or therapeutic options for patients.

overall_design: RNAseq profiling of purified trophoblast (CTB) with different inhibitors with or without 5-HT at 48h (serotonylation and serotonin transport inhibitor).

middle: S

first: Seth

last: Guller

first: Zhonghua

last: Tang

first: Yuan-Wei

last: Zhang

first: Erin

middle: C

last: Siegman

first: Kristin

last: Milano

first: Gary

last: Rudnick

first: Harvey

last: Kliman


title: Epigenetically mediated drug resistance in myeloma is coordinated by a myeloma-associated long non-coding RNA PLUM [RNA]

first: Yinghui

last: Li

overall_design: KMS-11 PLUM knock-down followed by RNA-seq (control/treated triplicates), H3K27me3 ChIP-seq (control/treated triplicates) and EZH2 ChIP-seq (endogenous duplicates)

first: Kamalakshi

last: Deka

first: Jean-Michel

last: Lee


title: REGION-SPECIFIC GENE EXPRESSION AND SEX INFORM ABOUT  DISEASE SUSCEPTIBILITY IN THE AORTA  - MCAM Knockdown

city: Los Angeles

first: Feiyang

last: Ma

state: CA

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

institute: UCLA

summary: Pathology in large vessels frequently develops at specific locations, implying that local stressors and spatially restricted gene expression are likely contributors to disease susceptibility. To identify site- and sex-specific differences that could inform about vulnerability, we performed single-cell transcriptomics in the carotids, aortic arch, thoracic, and abdominal aorta. Our findings revealed: (1) regionally defined transcriptional profiles, (2) signatures associated with embryonic origins, and (3) differential contributions of sex-specific effectors. Sex differences were predominantly observed in the thoracic and abdominal aorta. MCAM/CD146, a transcript with sex-skewed expression in vSMC of the abdominal aorta showed a 2.5-fold lower expression in males when compared to females. siRNA knockdown was performed to identify downstream targets of MCAM in vascular smooth muscle cells and to assess if sex affected number and biological function of genes modulated by changes in MCAM expression. MCAM was found to be further downregulated in vSMC associated with aortic aneurysms in humans. The findings reveal underlying diversity within vSMC populations with relevance to understanding site-specific and sex-specific variation of vascular pathologies.

overall_design:
Gene expression profiling analysis of RNA-seq data from vascular smooth muscle cell lines 40 hours following transfection with either control or MCAM siRNA. All samples prepared in duplicate, with six distinct vSMC donors (3M/3F). A subset of samples were used as non-transfected controls
PCZ16,G88 and LN983 are female Samples. T79, R88 and G82 are male Samples.

first: Milagros

last: Romay

first: Maria-Luisa

last: Iruela-Arispe


title: Ras-related protein 2 limits vascular smooth muscle cell phenotypic switching and abdominal aortic aneurysm development

status: Public on Jun 29 2025

city: Nanjing

first: Shanshan

last: Luo

state: Jiangsu province

address: Long Mian Avenue 109

department: Pharmacy

institute: 南京医科大学

summary: Abdominal aortic aneurysm (AAA) and the attendant catastrophic event of rupture remain a leading cause of death.  During AAA, VSMCs lost contractile-related phenotype, with reduced levels of actin alpha 2, smooth muscle (ACTA2), transgelin (TAGLN) and calponin 1 (CNN1)) , and obtain ability to secrete matrix metalloproteinases to degrade the extracellular matrix and weaken the arterial wall, which potentiate the rupture of the aneurysm. Angiotensin 2 (Ang II) can induce phenotype transition of VSMCs，while the underlying mechanism remains elusive. Here we found Ang II treatment could reduce expression of R-Ras2, thus reducing the phosphorylation and nuclear translocation of TFII-I, as a result, the gene expression of ACTA2, TAGLN and CNN1 were inhibited and VSMCs lost the contractile phenotype.

overall_design: RNA-seq profile of HASMCs stimulated with PBS or Ang II

first: Yong

last: Ji

first: Ke

last: Zhong


title: Epigenetically mediated drug resistance in myeloma is coordinated by a myeloma-associated long non-coding RNA PLUM

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

overall_design: Refer to individual Series


title: POSITIONAL TRANSCRIPTOMICS SHED LIGHT ON SITE-SPECIFIC PATHOLOGIES OF THE AORTA

summary: Pathologies of large vessels, such as atherosclerosis and aneurysms tend to develop at specific sites in the vascular tree. The consistency with which these events emerge suggests that a combination of unique local stressors, particularly physical forces and disturbances in gene expression profiles underlies disease etiology. We sought to investigate whether transcriptional diversity in specific segments of the aorta could be used to identify emergence of site-restricted vascular disease. Transcriptional profiling was performed using single cell RNA-seq in the carotids, aortic arch, thoracic and abdominal aorta across both sexes. Analyses of the data identified sex-invariant region-specific differences that were further validated by immunocytochemistry. Analysis of vascular smooth muscle cell transcriptomics from distinct regions of the aorta and carotids showed a high degree of similarity, but also uncovered skewed expression of a small percentage of transcripts (7.2%) towards particular vascular segments (carotid, aortic arch, thoracic and abdominal aorta). In silico cross-reference of genes known to be associated with vascular disease with the unique transcriptional signatures validated our proposed hypothesis. Specifically, we found correlations between localized-diseased causing GWAS candidate genes and region-enriched signatures. Pair-wise comparison between anatomic regions across sexes identified regional sex-specific gene signatures highlighting prominent regional-sex dependent differences were observed in vSMCs of the thoracic and abdominal aorta, consistent with sex-specific burden of aneurysm in these regions. Of these regional sex-enriched candidates’, Mcam/CD146, showed ventral thoraco-abdominal distribution, enriched expression in females and it was significantly reduced in the AngII / hypercholesterolemic model of aortic aneurysm. Furthermore, induction of aneurysms in mice lacking Mcam/CD146 resulted in larger lesions and accelerated death due to dissection.

overall_design: Carotid arteries and aorta spanning the aortic root to the iliac bifurcation were isolated from 12 week old female and male mice and dissected into 4 segments based on anatomic landmarks.  Samples were segregated by sex and anatomic location and digested into single cell preperations prior to library preperation.

first: M

middle: L


title: RCOR2 downregulates CIITA via HDAC1-mediated histone deacetylation in cancer cells [ChIP-seq]

status: Public on Jun 28 2025

city: Dallas

first: Lei

last: Bao

address: 5323 Harry Hines Blvd, NB6.126

institute: UT Southwestern Medical Center

summary: RCOR2 and HDAC1 directly co-binds to CIITA gene. RCOR2 knockout does not affect HDAC1 binding on CIITA gene. RCOR2 has no binding on most MHCII genes.

overall_design: MDA-MB-231 cells overexpressing HA tagged RCOR2 were subjected to ChIP-seq with anti-HA antibody. Parental and RCOR2-KO MDA-MB-231 cells were subjected to ChIP-seq with anti-HDAC1 antibody. Occupancy of RCOR2 and HDAC1 on CIITA and MHCII genes were analyzed.

first: Weibo


title: Effect of RCOR2 in cancer cell stemness and immune evasion

summary: To investigate the function of RCOR2 in cancer cell stemness and immune evasion, we established RCOR2-KO MDA-MB-231 cells by CRISPR-Cas9. We then performed gene expression profiling analysis using data obtained from RNA-seq of the parental cells as well as two independent KO cell lines. Two biological repeats were applied for each cell line.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for parental and RCOR2-KO MDA-MB-231 cells.


title: Kimchi intake promotes antigen-presenting cell signaling and CD4⁺ T cell remodeling without inducing systemic immune activation: A single-cell RNA-seq substudy of a randomized, double-blind, placebo-controlled clinical trial

city: Gwangju

first: Wooje

email: wjlee@wikim.re.kr, ntinamu001@gmail.com

address: 86, Kimchi-ro, Nam-gu

country: South Korea

institute: World Institute of Kimchi

summary: This study aimed to investigate the systemic immunological effects of kimchi consumption in humans. We conducted a 12-week randomized, double-blind, placebo-controlled clinical trial involving thirteen overweight but otherwise healthy adults who consumed either placebo, spontaneously fermented kimchi (S-K), or starter kimchi fermented with Leuconostoc mesenteroides KCKM0828 (LMS-K). Peripheral blood mononuclear cells (PBMCs) were collected before and after the intervention and subjected to single-cell RNA sequencing (scRNA-seq) to profile immune responses at single-cell resolution.

overall_design: Thirteen overweight but otherwise healthy adults (BMI 23–30 kg/m²) were enrolled in a 12-week randomized, double-blind, placebo-controlled trial of kimchi consumption (ClinicalTrials.gov: NCT05898802). Participants were randomized to placebo (n = 4), spontaneously fermented kimchi powder (S-K; n = 5), or starter-fermented kimchi powder prepared with Leuconostoc mesenteroides KCKM0828 (LMS-K; n = 4). Peripheral blood mononuclear cells (PBMCs) were collected at two time points per subject—baseline (pre-intervention) and post-intervention (week 12)—yielding 26 samples.  Cryopreserved PBMCs were thawed, washed, and counted, then multiplexed via antibody-conjugated poly(A) DNA barcodes. Single cells were captured and barcoded on the BD Rhapsody HT Xpress system, followed by cDNA synthesis on mRNA-capture beads. Whole-transcriptome and sample-tag libraries were constructed using the BD Rhapsody WTA amplification kit and sequenced on an Illumina NovaSeq X Plus (2 × 100 bp, paired-end). Raw FASTQ files were processed with the BD Rhapsody WTA Analysis Pipeline v2.2.1 and aligned to GRCh38 for downstream single-cell analyses.

first: Sung Wook

last: Hong


title: RCOR2 downregulates RNF43 via LSD1-mediated histone demethylation in cancer cells

summary: RCOR2 and LSD1 directly co-binds to RNF43 gene. RCOR2 knockout does not affect LSD1 binding on RNF43 gene.

overall_design: Parental and RCOR2-KO MDA-MB-231 cells were subjected to CUT&RUN with anti-LSD1 antibody. CUT&RUN libraries with anti-normal rabbit IgG were used as input for analysis. Occupancy of RCOR2 and LSD1 on RNF43 gene was analyzed.


title: RNA sequencing of mouse cardiac neutrophils after myocardial ischemia and reperfusion injury model

city: Tsukuba

first: Chigusa

last: Nakahashi-Oda

state: Ibaraki

address: 1-1-1 Tennodai

department: Immunology

country: Japan

institute: University of Tsukuba

summary: We performed bulk RNA-seq of cardiac neutrophils from the heart of WT and Cd300a-/- mice 3 days after  myocardial ischemia and reperfusion.

overall_design: CD45.2+ CD11b+ Ly6G+ SiglecF+ neutrophils and CD45.2+ CD11b+ Ly6G+ SiglecF- neutrophils were isolated using flow cytometry from heart of WT and Cd300a-/- mice 3 days after Myocardial ischemia and reperfusion. Eight hearts were pooled per each sample.

first: N

last: Nishiyama

first: T

last: Sugasawa

first: C

first: A

last: Shibuya


title: Transcriptional differences in Bradyrhizobium sp. USDA 3456 during growth on methanol with La versus succinate with La

status: Public on Jun 27 2025

city: Berkeley

first: Charlotte

middle: Charlie

last: Mineo

address: 421 Koshland Hall

department: Plant and Microbial Biology

institute: UC Berkeley

summary: Nodule-forming bacteria play crucial roles in plant health and nutrition by fixing atmospheric nitrogen. Despite the importance of this relationship, how nodule-forming bacteria are affected by plant exudates and soil minerals is not fully characterized. Of particular interest are the effects of plant-derived methanol and lanthanide metals on the growth of nitrogen-fixing Rhizobiales. Prior work has demonstrated that select Bradyrhizobium are able to assimilate methanol only in the presence of lanthanide metals; however, the pathway enabling assimilation remains unknown. Here we characterize Bradyrhizobium sp. USDA 3456 to determine the pathways involved in methanol metabolism. Based on genomic analyses, we hypothesized that methanol assimilation in these organisms occurs via the lanthanide-dependent methanol dehydrogenase XoxF, followed by oxidation of formaldehyde via the glutathione-linked oxidation pathway, subsequent oxidation of formate via formate dehydrogenases, and finally assimilation of CO2 via the Calvin Benson Bassham (CBB) pathway. Transcriptomics revealed upregulation of the aforementioned pathways in Bradyrhizobium sp. USDA 3456 during growth on methanol. Assays demonstrated increased activity of the glutathione-linked oxidation pathway and formate dehydrogenases during growth on methanol compared to succinate. 13C-labeling studies demonstrate the presence of CBB intermediates and label incorporation during growth on methanol. Our findings provide multiple lines of evidence supporting the proposed XoxF-CBB pathway and, combined with genomic analyses, suggest that this metabolism is widespread among Bradyrhizobium and Sinorhizobium species.

overall_design: To identify genes involved in methanol metabolism, Bradyrhizobium sp. USDA 3456 grown in the presence of 10 µM lanthanum chloride with either succinate or methanol as a carbon source.  Cells were harvested during mid-exponential growth and RNA extraction and RNA-seq analyses were performed. Three replicates are provided for each condition.

last: Martinez-Gomez


title: Sustained Mesenchymal Reprogramming of Endothelial Cells after Completion of Chemotherapy [ChIP-seq]

status: Public on Jun 26 2025

city: Kansas City

first: Eugene

last: Konorev

state: MO

address: 1750 Independence Ave

institute: Kansas City University

summary: Cardiovascular disease is the prevailing cause of death among cancer survivors. Remarkable increase in cardiac disease burden in this group is likely due to the effects of cancer itself and, especially, cardiotoxic cancer treatments. Of the cardiotoxic cancer treatments, anthracyclines are notoriously known for causing vascular damage and severe cardiovascular complications. A defining feature of cardiac damage by doxorubicin (Dox), a prototypical anthracycline, is that it typically progresses after completion of chemotherapy. As the nature of delayed deterioration is not understood we focused in this study on the events that occur upon completion of chemotherapy. We adopted the Dox treatment/washout model to examine its lasting effects on endothelial cells. Our ChIP sequencing, transcriptomic, reporter plasmid, and Smad2/3 phosphorylation experiments demonstrated the enhanced activity of the canonical TGF-beta/activin pathway during Dox washout. Another notable feature was sustained mesenchymal reprogramming with significant upregulation of transcripts characteristic of fibroblastic and smooth muscle lineages. We utilized a selective ALK4/5/7 receptor kinase inhibitor, SB431542 (SB), to probe the role of the canonical TGF-beta/activin pathways in endothelial-to-mesenchymal reprogramming by Dox. When present during Dox washout, SB blocked increased expression of both mesenchymal transcripts and protein markers, and prevented cytoskeletal changes and fibronectin production by the treated endothelial cells. Cytoskeletal rearrangements led to increased endothelial monolayer permeability that was abolished by SB treatment. Thus, increased production of ALK4/5 receptor ligands, TGF-beta2 and activin, and heightened Smad2/3 activation response to these ligands during Dox washout leads to sustained mesenchymal reprogramming of endothelial cells and compromised endothelial barrier function.

overall_design: ChIP seq of Smad3 in human umbilical vein endothelial cells (HUVEC) after doxorubicin treatment followed by its washout.

first: Kass

last: Sjostrom

first: Shixin

last: Tao

first: Shannon

last: Landers

first: Amy

last: Kwok

first: Melissa

last: Cobb

first: Ria

last: Singh

first: Ralph

last: Shohet

first: Nataliya

last: Kibiryeva


title: Sustained Mesenchymal Reprogramming of Endothelial Cells after Completion of Chemotherapy [RNA-seq]

summary: Cardiovascular disease is the prevailing cause of death among cancer survivors. Remarkable increase in cardiac disease burden in this group is likely due to the effects of cancer itself and, especially, cardiotoxic cancer treatments. Of the cardiotoxic cancer treatments, anthracyclines are notoriously known for causing vascular damage and severe cardiovascular complications. A defining feature of cardiac damage by doxorubicin (Dox), a prototypical anthracycline, is that it typically progresses after completion of chemotherapy. As the nature of delayed deterioration is not understood we focused in this study on the events that occur upon completion of chemotherapy. We adopted the Dox treatment/washout model to examine its lasting effects on endothelial cells. Our ChIP sequencing, transcriptomic, reporter plasmid, and Smad2/3 phosphorylation experiments demonstrated the enhanced activity of the canonical TGF-b/activin pathway during Dox washout. Another notable feature was sustained mesenchymal reprogramming with significant upregulation of transcripts characteristic of fibroblastic and smooth muscle lineages. We utilized a selective ALK4/5/7 receptor kinase inhibitor, SB431542 (SB), to probe the role of the canonical TGF-/activin pathways in endothelial-to-mesenchymal reprogramming by Dox. When present during Dox washout, SB blocked increased expression of both mesenchymal transcripts and protein markers, and prevented cytoskeletal changes and fibronectin production by the treated endothelial cells. Cytoskeletal rearrangements led to increased endothelial monolayer permeability that was abolished by SB treatment. Thus, increased production of ALK4/5 receptor ligands, TGF-2 and activin, and heightened Smad2/3 activation response to these ligands during Dox washout leads to sustained mesenchymal reprogramming of endothelial cells and compromised endothelial barrier function.

overall_design: RNA seq profiling of 1) human umbilical vein endothelial cells response to doxorubicin treatment; 2) human umbilical vein endothelial cells transcriptome change upon washout after doxorubicin treatment; and 3) response of control (scrambled shRNA) and Smad3 deficient (Smad3 shRNA) human cardiac microvascular endothelial cells to TGF-beta2 treatment.


title: Heritable Tissue-Specific Gene Expression Associates With Chronic Wound Microbial Species

city: Lubbock

first: Khalid

last: Omeir

state: Texas

address: 2901 Main St.

department: Department of Biological Sciences

institute: Texas Tech University

summary: The reasons for interpatient variability in chronic wound microbiome composition are thought to be complex but are poorly known. To investigate how patients’ genetically regulated tissue expression may influence chronic wound bacterial composition, we performed a microbiome-transcriptome-wide association study. This approach involved estimating for 509 patients their tissue-specific gene expression from DNA genotypes, followed by associating gene expression to the relative abundances of species detected in their wounds as provided on clinical reports to the physician. Comparisons to artery, blood, fibroblast, skeletal muscle, skin, subcutaneous fat, and nerve tissue resulted in 251 transcriptional differences at 109 genes significantly explaining abundances of 39 different species. Overall, these species were detected in 63% of wounds. A similar number of associations per tissue was observed (range 31-39) and many genes were associated at multiple tissues in distinct ways. The cumulative variance across loci for species relative abundance explained ranged from ~5-36%, depending on species. Although the same gene was almost never associated with more than one species, ~14% of enriched pathways were independently enriched for multiple species, which may reflect the diversity of ways microbes interact with partially overlapping attributes of the wound bed. Commonly enriched pathways pertained to collagen formation and modification, cell signaling, cytoskeletal dynamics, interactions with extracellular matrix, transmembrane proteins, among others. This work expands the new perspective that individual genetics may partially determine microbial colonization and infection.

overall_design: DNA was extracted from buccal swabs to genotype patients, from which gene and intron retention levels were estimated for biologically relevant tissue types. Subsequently, tissue-specific expression was associated to chronic wound bacterial abundance.

first: Jacob

last: Ancira

first: Rebecca

last: Gabrilska

first: Craig

last: Tipton

first: Clint

last: Miller

first: Ashley

last: Noe

first: Kumudu

last: Subasinghe

first: Megan

last: Rowe

first: Nicole

last: Phillips

first: Joseph

last: Wolcott

first: Caleb

middle: D

last: Philips


title: Myeloid mimicry mediates hyperprogression in patients with renal medullary carcinoma treated with nivolumab plus ipilimumab

first: Pavlos

last: Msaouel

address: 1155 Pressler Street, Unit 1374

department: Genitourinary Medical Oncology

institute: The University of Texas MD Anderson Cancer Center

summary: Renal medullary carcinoma (RMC) is a rare but highly aggressive malignancy that mainly afflicts young individuals of African descent and has few treatment options. Despite the approval of combination immune checkpoint therapy (ICT) for other kidney cancers, its efficacy against RMC remains elusive. We conducted a prospective clinical trial of nivolumab plus ipilimumab in patients with RMC. Enrollment was halted for futility after a prespecified interim analysis revealed that all 10 patients experienced rapid disease progression with 5/10 meeting radiological criteria for hyperprogression. Median progression-free survival was only 1.38 months (95% confidence interval (CI): 1.28, 1.60). To elucidate the underlying mechanisms, we analyzed high-quality single-cell RNA sequencing data from RMC patients before and after nivolumab plus ipilimumab treatment. Our analysis suggested that ICT-triggered interferon gamma upregulation induces RMC tumor cells to activate key myeloid regulators such as the CEBPB / p300 complex that promote tumor cell proliferation leading to hyperprogression. Using an immunocompetent somatic mosaic genetically engineered mouse model of RMC, we confirmed that combination ICT induced hyperprogression of primary and metastatic tumors compared with IgG control by hijacking myeloid-affiliated transcriptional circuits. Blocking of this “myeloid mimicry” adaptive mechanism using a selective inhibitor of p300 induced sensitivity to combination ICT in our animal model of RMC. These findings provide novel insights into RMC adaptation to ICT and demonstrate that inhibiting master myeloid regulators can elicit antitumor responses to ICT thus informing the next generation of immunotherapy strategies targeting hyperprogression.

overall_design:
We collected samples from a total of 15 patients. 9 patients provided samples for single-cell RNA (scRNA) sequencing, and 6 other patients provided samples for bulk-RNA sequencing. The scRNA samples consisted of fresh tumor biopsy tissues from 7 immunotherapy-naïve patients with Renal Medullary Carcinoma (RMC), and tissues from 2 patients with RMC collected immediately after aggressive progression on nivolumab plus ipilimumab. The bulk-RNA samples included 3 baseline samples and 3 samples from patients with RMC collected after aggressive progression on nivolumab plus ipilimumab treatment.
contributor: Moon Shots Cancer Genomics Laboratory (CGL)
contributor: MD Anderson institutional Advanced Genomics Technology Core (AGTC)

***************************************************************
Raw data is not provided due to patient privacy concerns.
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first: Jianfeng

last: Chen

first: Xinmiao

last: Yan

first: Jianjun

last: Gao

first: Linghua

last: Wang

first: Giannicola

last: Genovese


title: PROLIFERATIVE STEM CELL LIKE POPULATION OF BLASTS IN KMT2A REARRANGED INFANT ALL

city: oxford

first: Thomas

last: Jackson

address: weatherall institute of molecular medicine

department: paediatrics

institute: University of Oxford

summary: Among pediatric acute lymphoblastic leukemias (ALL), KMT2A-rearranged infant ALL (KMT2Ar iALL) carries a uniquely poor prognosis due to high rates of treatment-refractory or relapsing disease. It is important to understand how KMT2A mutations drive such aggressive disease in order to develop more effective and less toxic therapies. The PROM1 gene, encoding the pentaspan glycoprotein prominin-1/CD133, is activated by the direct action of the most common KMT2A fusion protein; KMT2A::AFF1 (MLL-AF4). CD133 expression is essential for proliferation of KMT2A::AFF1+ cell lines but its role in primary disease remains unclear with heterogenous expression seen in iALL patient samples. To clarify the role of CD133 in KMT2Ar iALL we have used a highly physiological primary human fetal liver derived model (CRISPRKMT2A::AFF1 ALL) which recapitulates CD133 heterogeneity. We show that CD133 expression marks a highly proliferative subset of CRISPRKMT2A::AFF1 blasts with a stem-cell gene expression profile capable of causing more aggressive disease in vivo. CRISPR inactivation of PROM1 limits leukemic proliferation, suggesting a functional role in our model and providing a strong rationale for targeting therapies against CD133.

overall_design: RNA-seq of fetal derived MLL-AF4 iALL model

first: Joe

last: W Cross

first: Lucy

last: Field

last: Hamer

first: Alastair

last: Smith

first: Nicholas

last: T Crump

first: Siobhan

last: Rice

last: Harman

last: Ling

first: Natalina

last: Elliott

first: Qinqing

middle: Q

last: Wu

first: Nouhad

last: El Ouazzani

last: Thomas

first: Sarah

last: Inglott

first: Jack

last: Bartram

first: Irene

last: Roberts

last: Milne

first: Anindita

last: Roy


title: Spatially resolved chimeric analysis reveals extracellular CKB-mediated ATP uptake at the glioma-astrocyte invasive front

city: 成都

first: ping

last: he

address: 17 Renmin South Road, Wuhou District, Chengdu

institute: sichuan university

summary: Glioblastoma (GBM) is a highly invasive primary brain tumor that, although rarely metastasizing outside the brain, frequently infiltrates surrounding brain tissue. This infiltrative growth may exploit the brain’s metabolic support system, which involves various brain-resident cells providing essential nutrients and maintaining energy balance. In this study, we investigated the metabolic dependencies of infiltrative GBM cells by combining spatially resolved transcriptomic profiling with advanced computational methods in xenografted GBM models. Our findings reveal that GBM cells upregulate creatine kinase brain type (CKB) at the leading edge to adapt to local energy deprivation. CKB facilitates the conversion of creatine to phosphocreatine, utilizing ATP supplied by astrocytes to support tumor cell survival and invasion. Targeting CKB with cyclocreatine significantly reduced tumor size and restricted infiltrative growth in vivo, indicating that GBM cells utilize CKB to harness extracellular ATP via the creatine pathway. These findings suggest that targeting CKB in GBM may offer a novel therapeutic strategy to combat infiltrative growth in this aggressive cancer.

overall_design: We generated and analyzed spatially resolved RNA profiles in two GBM models: a GSC xenograft model and a TP53, NF1, and PTEN (TNP)-inactivated human neural stem cell-derived model. This approach enabled us to dissect tumor and tumor microenvironment (TME) interactions across spatial contexts.


title: Azanucleoside treatment leads to B cell leukemia in Rag1 deficient mice

city: Bethesda

first: Peter

last: Aplan

state: Maryland

address: 37 convent drive

department: Genetics

institute: CCR-NCI-NIH

summary: 5-Aza-4’-thio-2’-deoxycytidine (ATC) is an azanucleoside cytidine analog used in preclinical studies for solid tumors as a promising DNA methyltransferase 1 (DNMT1) inhibitor. Repeated treatment with ATC has previously been shown to result in acute lymphoblastic leukemia (ALL) of both B-cell and T-cell origin in mice. Herein, Rag1 knockout mice were treated with ATC to determine if ATC could be oncogenic in non-lymphoid cells. However, ATC treatment targeted early B progenitors and invariably led to B-lineage ALL, with a gene expression signature similar to human B cell precursor (BCP) ALL. Whole exome sequencing revealed numerous single base substitutions of cytosine, primarily C>G transversions at CpG dinucleotides, within genes important for BCP-ALL. Bisulfite sequencing and treatment with a non-covalent DNMT1 inhibitor indicated that methylated cytosines were preferred targets for mutagenesis. This study reveals that ATC exposure leads to both DNMT1 dependent and independent mutagenesis and provides a direct link from ATC exposure to complex mutation signature to malignant transformation

overall_design: We used Bulk RNA Sequencing for comparison between expression profiles between BCP-ALL and non-leukemic counterpart, we used Rag1 KO BCP ALL samples(N=6), CD19+B220+ sorted Rag1 BM cell samples (N=3) and B220+ sorted Rag1 BM cell samples (N=2).

first: Vijay

last: Negi

first: Ryan

last: Bertoli


title: Genome-wide CRISPR screen identifies Menin and SUZ12 as regulators of human developmental timing [CUT&RUN]

city: New York

first: Hyein

middle: Sophia

last: Cho

state: NY

address: 430 E 67th St

department: Developmental Biology

institute: Memorial Sloan Kettering Cancer Center

summary: Embryonic development follows a sequence of events that is broadly conserved across species, yet the pace of development is highly variable. Compared to most other species, humans exhibit a slower pace that is largely recapitulated in in vitro stem cell models, suggesting a cell-intrinsic clock that tracks time. Using the directed differentiation of human embryonic stem cells (hESCs) into neuroectoderm as a proxy for developmental timing, we performed a whole-genome CRISPR-Cas9 screen and found that epigenetic factors MEN1 and SUZ12 modulate the speed of hESC neural differentiation. Genetic and pharmacological loss-of-function of MEN1 or SUZ12 accelerates the acquisition of neural fate by altering the balance of activating H3K4me3 and repressive H3K27me3 chromatin modifications at bivalent promoters and thereby priming a faster activation of developmental genes upon differentiation. The acceleration effect is also observed in definitive endoderm, cardiomyocyte, and neuronal differentiations. These results indicate that chromatin bivalency acts a general driver of human-specific timing across all major germ layers and developmental stages. Furthermore, our study uncovers a novel functional cooperation between MEN1 and SUZ12 as a key mechanism for the temporal regulation of developmental programs.

overall_design: CUT&RUN sequencing study of hESC-derived neuroectoderm cells, NT, MEN1 KO, SUZ12 KO

last: Xu

first: Lorenz

last: Studer


title: Polyploid cisplatin-resistant cancer cells have altered nuclear organization and epigenomic status

city: Baltimore

first: Anna

last: Gonye

address: 733 N. Broadway

institute: Johns Hopkins University School of Medicine

summary: Chemotherapy resistance remains a critical barrier in cancer treatment, partly driven by polyploid cells that survive therapy and contribute to tumor recurrence. Here, we investigated epigenomic and transcriptional changes associated with cisplatin-surviving polyploid cells compared to parental cancer cells in prostate cancer (PC3) and triple-negative breast cancer (MDA-MB-231) cell lines. We observed persistent dysregulation of chromatin compaction and altered nuclear structure in polyploid cells following cisplatin treatment. Genome-wide chromatin accessibility profiling via ATAC-seq revealed significant remodeling, notably decreased promoter accessibility at proliferation-associated loci and increased accessibility of distal regulatory elements linked to inflammation and stress response. RNA-seq analyses demonstrated a coordinated transcriptional shift away from proliferative signatures toward inflammatory and survival pathways, including activation of NFκB, interferon response, and integrated stress response pathways. Importantly, we identified subsets of genes showing concordant changes in promoter accessibility and transcriptional activity, directly linking chromatin remodeling to transcriptional reprogramming. These integrated findings highlight the role of chromatin dynamics and epigenetic plasticity in chemotherapy resistance, demonstrating that widespread chromatin accessibility changes facilitate the transition to a stress-adapted, polyploid cell state. This study provides new insights into the molecular mechanisms supporting cancer cell persistence after chemotherapy.

overall_design: MDA-MB-231 (breast cancer cell line) and PC3 (prostate cancer cell line) were treated with cisplatin. Surviving cells were analyzed 1 and 10 days post-treatment removal (PTR). Bulk ATAC-sequencing was performed on untreated cell lines and surviving cells 1 and 10 days PTR in biological triplicate.


title: Matric and osmotic stress have overlapping effects on Variovorax beijingensis transcription

city: Houston

first: Jonathan

middle: J.

last: Silberg

address: 6100 Main St

institute: Rice University

summary: Soil microbes must continuously adapt to changes in water availability, which dynamically fluctuates with weather and irrigation, and these adaptations are closely linked to climate effects. Soil water potential, which regulates microbe-available water, is controlled by both osmotic and matric potential, which both increase as soils dry. While both parameters can independently increase water potential, the genetic mechanisms of microbial response are unknown, with potentially different mechanisms available for microbes to respond to changes in soil osmolyte concentrations versus changes in water availability within a textured material. To explore microbial responses to matric versus osmotic potential shifts, we evaluated the activity, persistence, and transcription of Variovorax beijingensis in soils and liquid cultures subjected to either matrix or osmotic stress. We find this microbe respires in dilute minimal medium (-240 ±104 kPa), in liquid medium supplemented with sucrose (-1323 ±20.8 kPa), and in a pair of matrices that span a similar range of pressures (-183 ±55 and -1393 kPa ±200 kPa). Using principal-component analysis, we show that gene expression varies significantly across all four conditions, even in cases where the pressure is similar. However, the direction of gene expression changes arising from an increase in osmotic pressure within liquid medium and an increase in matric potential within the different soils covaried for 68% of the transcripts. Thus, as Variovorax transitions from conditions of low to high osmotic or matric potential, which both decrease water availability, there is large overlap in the transcriptional response, although the responses are not identical.

overall_design: V. beijingensis was grown in liquid mM9 (low osmotic potential), mM9 with 425 mM sucrose (high osmotic potential), artificial soil Q2 (low matric potential), and artificial soil M2 (high matric potential) for 72 hours in six replicates. The total RNA was extracted (followed by rRNA depletion), and the library was prepared for RNA-seq.

first: Jiwoo

last: Kim

first: Bjorn

last: Shockey

first: Kirsten

last: Hofmockel

first: Caroline

last: Masiello


title: Genome-wide CRISPR screen identifies Menin and SUZ12 as regulators of human developmental timing.

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

overall_design: Refer to individual Series


title: Genome-wide CRISPR screen identifies Menin and SUZ12 as regulators of human developmental timing [RNA-seq]

overall_design: Bulk RNA-seq study of hESC-derived neuroectoderm cells, NT, MEN1 KO, SUZ12 KO


title: Genome-wide CRISPR screen identifies Menin and SUZ12 as regulators of human developmental timing [ATAC-seq]

overall_design: ATAC-seq study of human embryonic stem cells, NT, MEN1 KO, SUZ12 KO


title: Biomarker Identification via Spatial Transcriptomics Profiling of Colorectal Cancer and Colorectal Cancer with Liver Metastasis Stem Cells

city: cheonan

first: Dongjun

last: Jeong

state: Chungcheongnam-do

address: 25, Bongjeong-ro, Dongnam-gu

institute: Soonchunhayng Unvi.

summary: The survival rate of patients with colorectal cancer (CRC) declines sharply with recurrence and metastasis. Cancer stem cells play a crucial role in the initiation, progression, recurrence, and metastasis of colorectal cancer. Therefore, in this study, we aimed to identify the CRC-associated genes via spatial analyses of normal colon tissue, colorectal cancer tissue, and colorectal cancer liver metastasis using NanoString GeoMx digital spatial profiling.

overall_design: The TMA slide comprised 59 samples, including 40 cores of CRC (primary cancer), 10 cores of CRC with liver metastasis, and nine cores of normal colon tissue (adjacent to cancer). We selected samples from patients with CRC who had normal colon tissue, primary colorectal cancer tissue, and colorectal cancer with liver metastasis tissue. To identify tumors and cancer stem cells, CD44 and EpCAM staining was performed. EpCAM+/CD44- cells were used as markers to identify non-CRCSCs, and EpCAM+/CD44+ cells were used as markers to identify CRCSCs.

first: Jeong-An

last: Gim

first: Minho

last: Lee

first: Sooyoun


title: MUC1-C IS ESSENTIAL FOR ESTABLISHING AND RECALLING INFLAMMATORY MEMORY OF OSIMERTINIB RESISTANCE IN NSCLC CELLS [H1975_vs_H1975-OR]

city: Fukuoka

first: Naoki

last: Haratake

state: Please Select

address: 3-1-1 Maidashi, Higashi-ku

institute: Graduate School of Medical Sciences, Kyushu University

summary: MUC1-C is necessary for establishing and recalling resistance of NSCLC cells to osimertinib by driving an inflammatory memory responseThe oncogenic MUC1-C protein functions as a master regulator of NSCLC cell resistance to osimertinib by unclear mechanisms. We report that MUC1-C-mediated regulation of STAT1 and the interferon (IFN) type I/II pathways is necessary for establishing osimertinib resistance. Studies of osimertinib-resistant NSCLC cells selected for growth in the absence of drug further demonstrate that revertant cells are dependent on MUC1-C for recalling resistance to osimertinib. We show that establishing and recalling osimertinib resistance is dependent on activation of the MUC1 gene at (i) a proximal enhancer-like signature 1 (pELS-1) by MUC1-C and STAT1 and (ii) a pELS-2 by MUC1-C, JUN/AP-1 and PBAF. The MUC1 pELS regions function as memory domains for activation of MUC1-C and downstream STAT1 and IFN stimulated genes in conferring osimertinib resistance. Of clinical relevance, we report that the MUC1-C-driven inflammatory responses are induced in patient-derived, osimertinib-resistant MGH170 NSCLC cells with MET amplification. Our results further demonstrate that MGH170 cells are dependent on the MUC1-C-induced inflammatory response for resistance to the osimertinib and combination of osimertinib with the MET inhibitor capmatinib. These findings indicate that MUC1-C is necessary for establishing and recalling resistance of NSCLC cells to osimertinib by driving an inflammatory memory response.

overall_design:
Comparison between H1975, which is sensitive to osimertinib, and H1975-OR, which has become a resistance due to long-term exposure to osimertinib (H1975 vs H1975-OR).
Treatment of H1975 = None
Treatment of H1975-OR = Osimertinib


title: Single-cell multiomics reveals the oscillatory dynamics of RNA metabolism and chromatin accessibility during the cell cycle

status: Public on Jun 25 2025

city: Illkirch

first: Nacho

last: Molina

address: 1 Rue Laurent Fries

institute: Institut de génétique et de biologie moléculaire et cellulaire

summary: The cell cycle is a tightly regulated process that requires precise temporal expression of hundreds of cell cycle-dependent genes. However, the genome-wide dynamics of mRNA metabolism throughout the cell cycle remain uncharacterized. Here, we combined single-cell multiome sequencing, biophysical modeling, and  deep learning to quantify rates of mRNA transcription, splicing, nuclear export, and degradation. Our approach revealed that both transcriptional and post-transcriptional processes exhibit distinct oscillatory waves at specific cell cycle phases, with post-transcriptional regulation playing a prominent role in shaping mRNA accumulation. We also observed dynamic changes in chromatin accessibility and transcription factor binding footprints, identifying key regulators underlying the oscillatory dynamics of mRNA. Taken together, our approach  uncovered a high-resolution map of RNA metabolism dynamics and chromatin accessibility, offering new insights into the temporal control of gene expression in proliferating cells.

overall_design: Multiome profiling, snRNA-seq + snATAC-seq, of mouse embryonic stem cells culture in 2i and LIF in serum supplemented conditions

first: Maulik

middle: K

last: Nariya

first: David

last: Santiago-Algarra

first: Olivier

last: Tassy

first: Marie

last: Cerciat

first: Tao

last: Ye

first: Andrea

last: Riba


title: MUC1-C IS ESSENTIAL FOR ESTABLISHING AND RECALLING INFLAMMATORY MEMORY OF OSIMERTINIB RESISTANCE IN NSCLC CELLS [H1975-RT_vs_H1975-OR]

overall_design:
Comparison between H1975-OR, the osimertinib-resistant cell line, and H1975-RT cells, which had osimertinib removed for a longer period from H1975-OR and moderately regained sensitivity (H1975-OR vs H1975-RT).
Treatment of H1975-OR = Osimertinib
Treatment of H1975-RT = None


title: Characterizing heterogeneous cis-regulatory elements in gene regulatory programs associated with breast cancer

city: Tokyo

first: Kohei

last: Kumegawa

address: 3-8-31 Ariake, Koto-ku

institute: Japanese Foundation for Cancer Research

summary:
Background: Cis-regulatory elements (CREs) control oncogene expression and malignant phenotypes. The high clinicopathological heterogeneity of cancer cannot be explained by gene expression alone, being attributed to CRE heterogeneity. However, characterizing cancer-associated CRE is challenging. To address this issue, we performed a single-cell epigenomic analysis of clinical specimens.
Methods: To map the multicellular ecosystem of BC and identify candidate CREs (cCREs), we performed a single-cell assay for transposase-accessible chromatin with sequencing (scATAC-seq) of 38 prospectively collected breast cancer (BC) samples with various clinicopathological characteristics.
Results: First, we performed single-cell chromatin accessibility profiling of a high-quality set of 22,775 cells from BC samples. Cells were accurately annotated using marker gene accessibility and integration with existing single-cell RNA sequencing data. By predicting copy number variants, epithelial cells were classified into non-malignant and malignant cells. The chromatin accessibility patterns exhibited by malignant cells were consistent with the clinicopathological features of each tumor. We identified 224,585 cCREs across the BC ecosystem. By identifying cluster-specific differentially accessible cCREs (DA-cCREs) and constructing a putative enhancer-promoter network, we mapped the cis-regulatory landscape for cancer cells and the tumor microenvironment. In this dataset, we identified changes in the cis-regulatory landscape associated with cancer progression. In particular, estrogen receptor (ER)-positive tumors have increased accessibility of ER binding motifs during the cell transition from non-cancerous to cancerous and increased accessibility of Kruppel like factor motifs during the transition from cancerous to metastatic. Furthermore, the accessibility of putative enhancers targeting the same gene differed within or between tumors, highlighting intra- and inter-cis-regulatory tumor heterogeneity.
Conclusions: This study provides a valuable resource for future epigenetic research on BC and highlights the diverse regulatory landscape within or among tumor(s), suggesting that cCREs regulate tumor progression and intra- and inter-tumor heterogeneity.

overall_design:
Single-cell assay for transposase-accessible chromatin with sequencing (scATAC-seq) of 38 prospectively collected breast cancer (BC) samples with various clinicopathological characteristics.

***************************************************************
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: Chisa

last: Hori

first: Reo

last: Maruyama


title: 5-ALA photodynamic metabolite-powered zero-waste “ferroptosis amplifier” for enhanced hypertrophic scar therapy

status: Public on Jun 24 2025

city: Chongqing

last: Chen

address: No.426, Songshi North Road, Yubei District

institute: Stomatological Hospital of Chongqing Medical University

summary: Hypertrophic scar (HS) is a somatopsychic disease that significantly affects quality of life. 5-aminolevulinic acid (5-ALA)-mediated photodynamic therapy (PDT) holds promise for HS treatment, while challenges like poor transdermal delivery and rapid metabolism into non_xfffe_photosensitive heme restrict its effectiveness. Inspired by the natural phenomenon of a whale fall nourishing life, this study innovatively repurposes 5-ALA metabolic waste, heme, as a “whale-like” energy source to drive ferroptosis, thus establishing a zero-waste therapy. This is achieved by encapsulating 5-ALA and baicalin within human H-ferritin (HFn), subsequently incorporated into polyvinylpyrrolidone (PVP) microneedles (FAB@MN). The FAB@MN exhibits excellent targeting towards hypertrophic scar fibroblasts (HSFs) with pH-responsive programmed drug release. Upon application, 5-ALA is converted into PpIX to initiate PDT. Subsequently, baicalin is released, triggering ferroptosis while also synergizing with the ROS and heme accumulated during PDT to overstimulate the HO-1-heme metabolic axis. This activation releases Fe2+ and CO, further potentiating ferroptosis. Moreover, the enhanced ferroptotic response driven by FAB@MN induces mitophagy, leading to increased Fe²⁺ release from the mitochondria. Unlike conventional PDT only focuses on immediate effects, this approach uses 5-ALA photodynamic waste to fuel a sustained ferroptosis response post-PDT, offering new avenues for HS treatments.

overall_design: This research project has been approved by the Ethics Committee of Chongqing Medical University (CQHS-REC-2024-058). Nine HS tissues and the matched normal skin tissues were provided by patients undergoing surgical treatment, and each patient has voluntarily signed an informed consent form. All participants in this study did not have any known systemic diseases and were not receiving any treatments that could potentially affect the study results. In brief, tissues were first cut into 3 mm-thick slices, and then digested overnight with 0.25% neutral protease II. Subsequently, the epidermal layer was peeled off, and further digestion was carried out for 4-6 hours at 37°C with 0.2% Collagenase II. After digestion, cells were filtered and collected using a cell strainer with a 75μm pore size, then resuspended in Dulbecco's Modified Eagle Medium (DMEM) containing 10% FBS and cultured at 37°C in an atmosphere of 5% CO2. The method of isolating fibroblasts from normal skin was similar to the aforementioned process for obtaining HSFs with minor modifications. HSFs were seeded at a density of 1 × 10^5 cells/well in a 24-well plate and cultured for 24 hours in DMEM containing 10% FBS. Subsequently, the cells were treated with FAB NPs for 4 hours, followed by 10 mins of illumination, and then incubated for another 24 hours. Total RNA was extracted using TRIzol reagent (Invitrogen, USA), and the integrity of the RNA was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA). RNA samples were prepared using total RNA as a template. Initially, mRNA was extracted from total RNA using magnetic beads coated with poly-T oligonucleotides. This mRNA was then fragmented under high temperatures in the presence of divalent cations, using a 5X First Strand Synthesis Reaction Buffer. The synthesis of the first cDNA strand was achieved using random hexamer primers and M-MuLV Reverse Transcriptase (RNase H-). This was followed by the synthesis of the second cDNA strand using DNA Polymerase I and RNase H. Exonuclease and polymerase activities were employed to transform remaining overhangs into blunt ends. Subsequent to the adenylation of the 3' ends of the DNA fragments, adapters containing hairpin loop structures were attached, setting the stage for hybridization. cDNA fragments ranging in size from 370-420 bp were isolated using the AMPure XP system (Beckman Coulter, Beverly, USA). Amplification of these fragments was then carried out using Phusion High-Fidelity DNA Polymerase, along with universal PCR primers and an Index (X) Primer. The PCR products were purified within the AMPure XP system, and the library's quality was evaluated using an Agilent Bioanalyzer 2100 system. Indexed samples were clustered on the cBot Cluster Generation System using the TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufacturer's guidelines. Post-clustering, the library was sequenced on the Illumina Novaseq platform, producing 150 bp paired-end reads and thereby acquiring the sequence data of the fragments.

first: Yuan

first: Shan

last: Wang

first: Congxiu

last: Mao

first: Qinyi

last: Lu

first: Xingyu

last: Zhu

first: Dongqi

last: Fan

first: Yiping

last: Liu

first: Xu

first: Jinglei

last: Zhan

first: Zixin

last: Yang

first: Ping

last: Ji

first: Qingqing

last: He


title: Differential impact of inflammatory microglia signals and chronic HIV-1 Tat exposure on A1-like polarization of astrocytes

city: Philadelphia

first: Micheal

last: Nonnemacher

address: 245 N Broad St

institute: Drexel University

summary: In the context of neurodegeneration, activated microglia facilitate inflammation via secretion of TNF-α, IL-1α, and C1q. Astrocytes exposed to this signaling array polarize to a reactive inflammatory phenotype, termed A1 or A1-like. Astrocytes are essential for neuronal survival, synaptic support, and blood-brain barrier (BBB) function, but A1-like astrocytes upregulate inflammatory gene expression, downregulate neurotrophic factors, and secrete neurotoxic signals. The consequences of A1-like polarization on BBB function are unknown but may have etiological implications for some diseases. Frequently identified by upregulation of complement component 3 (C3), A1-like astrocytes have been characterized in neurodegenerative disorders like Alzheimer’s disease, with polarization correlated with disease progression and severity. However, the role of A1-like astrocytes in neurodegeneration associated with chronic viral infections, like HIV-1-associated neurocognitive disorder (HAND), remains unclear. An in vitro system using primary human astrocytes, as well as a BBB model featuring primary human brain microvascular endothelial cells (BMECs) co-cultured with astrocytes, was used to elucidate cellular and molecular consequences of chronic astrocyte activation. As measured by whole transcriptome analysis and protein expression assays, repeated treatment with TNF-α, IL-1α, and C1q induced A1-like polarization of astrocytes both in monoculture and in a BBB model, resulting in increased secretion of pro-inflammatory signals. No substantial change to BBB permeability was observed. In contrast, exposure to HIV-1 viral protein Tat did not independently induce A1-like polarization. Ongoing investigations into the effect of astrocyte polarization on BBB integrity and treatment with pathogenic proteins may provide insights into the role of neurotoxic astrocytes in neuroviral pathologies.

overall_design: To study these facets of astrocyte reactivity, an in vitro model of pro-inflammatory astrocyte polarization was developed using primary human fetal cells, both in monoculture and in a co-culture BBB model. An array of analyses, from RNA transcriptional profiles to changes in signal secretion, were used to characterize an A1-like phenotype in stimulated primary human astrocytes.

first: Jill

last: Lawrence

first: Will

last: Dampier

first: Joshua

last: Mell

first: Diehl

last: De Souza

first: Kayla

last: Schardien

first: Kyle

last: Yeakle

first: Jordan

last: Barnett

first: Bhaswati

last: Sen

first: Azad

last: Ahmed

first: Michael

last: Bouchard

first: Brian

last: Wigdahl


title: The deubiquitinase USP17 regulates the expression of the oncogenic driver β-catenin in colorectal cancer

city: Montreal

first: Marc

last: Servant

state: Quebec

address: P.O. Box 6128, Downtown Station

department: Faculty of Pharmacy

country: Canada

institute: Université de Montréal

summary: Aberrant activation of the Wnt/β-catenin signaling pathway is a hallmark of colorectal cancer (CRC). Here, we identify the deubiquitinating enzyme USP17 as a critical regulator of β-catenin stability in CRC. We demonstrate that USP17 directly interacts with and deubiquitinates β-catenin, preventing its degradation and enhancing its stability. CRISPR/Cas9-mediated knockout of USP17 in CRC-derived cell lines significantly reduced β-catenin levels and suppressed epithelial-mesenchymal transition (EMT), as evidenced by distinct morphological changes and altered expression of classical EMT markers. USP17 depletion reduced the proliferation of CRC cell lines and impaired CRC tumor growth in vivo. Conversely, USP17 overexpression in immortalized rat enterocytes elevated β-catenin levels and enhanced KRAS-induced cell proliferation. RNA sequencing and quantitative proteomic analysis of USP17-depleted CRC cells revealed significant suppression of the transcriptional coactivator function of β-catenin, impacting key oncogenic-related pathways. Our findings establish USP17 as a key regulator of β-catenin signaling and highlight its potential as a candidate therapeutic target in CRC.

overall_design: To gain mechanistic insight into how USP17 promotes CRC tumorigenesis, we performed bulk RNA sequencing of COLO 320DM cells transfected with independent USP17-targeting siRNA duplexes or non-silencing controls (siNT and L2)

first: Mariana

last: Acevedo

first: Florence

last: Dô

first: Firas

last: El-Mortada

first: Pierre-Luc

last: Tanguay

first: Laure

last: Voisin

first: Thibault

last: Houles

first: Geneviève

last: Lavoie

first: David

last: Allard

first: Philippe

middle: P

last: Roux

first: John

last: Stagg

first: Samuel

last: Doré

first: Logan

last: Walsh

first: Jimmy

last: Fourtounis

first: Eric

last: Bonneil

first: Sylvain

last: Meloche