title: Eukaryotic translation elongation factor EEF1G orchestrates the translational program to ensure meiotic progression in transcriptionally silent spermatocytes

city: Jinan

first: Jianze

last: Xu

state: Shandong

address: Jinan

institute: Shangdong university

summary: During meiotic prophase I, mammalian spermatocytes face a critical challenge that they need to synthesize recombination and synapsis proteins while global transcriptional suppression occurs at leptotene/zygotene stages. Here, we identify a spermatogenic cell highly expressed protein, eukaryotic translation elongation factor 1 gamma (EEF1G), as a master regulator of translational adaptation in mouse spermatocytes. Germ cell-specific Eef1g knockout causes complete male infertility due to the meiotic arrest at the zygotene stage, which is characterized by unresolved DNA double-strand breaks, failed homologous chromosome synapsis, and abolished crossover formation. Mechanistically, EEF1G can interact with ribosome proteins and RNA-binding factors. Ribosome profiling reveals that EEF1G deficiency reduces ribosome processivity, leading to ribosomal stalling and decreased protein production. Consequently, proteomic analyses show a specific decrease of synapsis (e.g., SYCP1/SYCE1) and recombination (e.g., MSH4/TEX11) proteins. This study establishes EEF1G as a critical coordinator of spatial translation in transcriptionally silent spermatocytes, bridging limited mRNA engagement to explosive protein synthesis for meiotic progression. Our work challenges traditional views of meiotic control by highlighting translation elongation, not just as a housekeeping process, but as a stage-specific regulator of germ cell development.

overall_design: RNA-seq analyses of the FACS-sorted leptotene and zygotene spermatocytes from 12 days postpartum (dpp). Breifly, cell lysis, mRNA reverse transcription, and cDNA amplification were performed using the Discover-sc WTA Kit V2 (Vazyme, N711). Subsequently, cDNA fragmentation and adapter ligation were carried out with the TruePrep Flexible DNA Library Prep Kit for Illumina (Vazyme, TD504). All procedures were conducted in strict accordance with the manufacturer's protocols. The Smart-seq2 library sequencing was performed by Novogene on Illumina platforms, generating 150 bp paired-end reads.

first: Xiaohua

last: Jiang

first: Hongbin

last: Liu


title: Ntlht1 Mutation Enhances Low Nitrogen Tolerance

status: Public on Sep 10 2025

city: Chengdu

first: liming

last: lu

address: No.211 Huimin Street

country: China

institute: Sichuan Agricultural University

type: Expression profiling by high throughput sequencing

summary: The results indicate that the NtLHT1 mutation enhances LN tolerance in tobacco. The contents of nitrate nitrogen and ammonium nitrogen, as well as the activities of nitrate reductase and glutamine synthetase, were greater in the mutants than in the wild type (WT). Moreover, the contents of some amino acids changed in the mutant. Transcriptome sequencing of roots under LN treatment revealed that the Ntlht1mutant presented 726 differentially expressed genes (DEGs). These DEGs were involved mainly in phenylpropanoid biosynthesis, starch and sucrose metabolism, and cysteine and methionine metabolism.

overall_design: The tobacco NtLHT1 mutant was hydroponically cultured in LN solution for 15 days. Then the roots from each material were collected, they were immediately stored in liquid nitrogen. After total RNA was extracted from the roots, the residual DNA was digested with DNase, and the mRNA was enriched to finish the library. Sequencing was performed after the library was constructed. The DESeq2 software package was used to screen for DEGs.

first: Qili

last: Mi

first: Ruhui

last: Li

first: Liming

last: Lu

first: Liqin


title: The SPN-4 Rbfox RNA-binding protein selects maternal mRNAs for CCR4-NOT-dependent clearance in C. elegans embryos

city: Minneapolis

first: Micah

last: Gearhart

state: MN

address: 6-160 Jackson Hall, 321 Church St.

department: Genetics, Cell Biology and Development

country: USA

institute: University of Minnesota

summary: The elimination of many maternal mRNAs is an essential feature of the maternal-to-zygotic transition. We report an essential pathway that clears many maternal transcripts from early C. elegans embryos using the RbFox-related SPN-4 RNA-binding protein as a specificity factor and the CCR4-NOT deadenylase complex as an effector. We biochemically identified SPN-4-associated mRNAs from late-stage oocytes and found that the set of SPN-4-associated transcripts is enriched for maternal mRNAs that undergo early decay. Single-molecule fluorescence in situ hybridization experiments established that many SPN-4-associated mRNAs fail to be eliminated in the absence of SPN-4. In the 3’UTRs of two target mRNAs, we identified RbFox motifs that bind SPN-4 in vitro and are required for SPN-4-dependent clearance in vivo. In a genetic screen to identify factors that work with SPN-4, we isolated alleles of CCR4-NOT components. Auxin-induced degradation of the LET-711/NOT1 scaffold and the CCF-1 deadenylase disrupted clearance of two SPN-4-associated transcripts. Our results support a model in which SPN-4 initiates expression in late-stage oocytes, associates with maternal mRNA targets through RNA sequences in their 3’UTRs and promotes CCR4-NOT-mediated decay during early embryogenesis.

overall_design: Transcripts present in cell lysates and immunoprecipitates from SPN-4, LIN-41, and OMA-1 ribonuclear protein complexes were profiled by RNA sequencing. An amplification method was utilized for low input RNA because of the restricted distribution of SPN-4 in the adult C. elegans gonad.

first: Tsukamoto

last: Tatsuya

first: Gearhart

last: Micah

first: Greenstein

last: David

first: Osborne Nishimura

last: Erin


title: Effect of Knockdown of POSTN on gene expression of Keloid Fibroblasts

city: Shenzhen

first: Cong

last: Huang

state: Guangdong

address: No. 1120, Lianhua Road, Futian District

institute: Peking University Shenzhen Hospital

summary: Here, we report that the knockdown of POSTN in fibroblasts leads to disruption in keloid inflammation. Moreover, molecules and pathway associated with extracellular matrix formation were impaired in POSTN-deficient fibroblasts. Therefore, our study highlights an indispensable role of POSTN in the pathogenesis of keloids.

overall_design: To examine the role and possible molecular mechanisms of POSTN on keloid fibroblasts, we subjected si-POSTN and si-CTL-transfected fibroblasts for RNA-seq analysis.

first: Fan

last: Zhuo

first: Bin


title: G-Quadruplex DNA suppresses Transcription during DNA Replication [CUT&Tag]

city: hefei

first: sun

last: xuedan

address: daoxiangcun

institute: ustc

type: Genome binding/occupancy profiling by high throughput sequencing

summary: G-quadruplex DNA (G4-DNA) structures play crucial but incompletely understood roles in coordinating DNA replication and transcription. Here, we investigate the dynamics of G4-DNA during DNA replication and its functional interplay with transcription machinery in synchronized tumor cells. Using a double-thymidine block to arrest cells in early S phase, we profile G4-DNA structures and associated transcription factors through CUT&Tag, while monitoring transcriptional changes via PRO-seq. To mechanistically dissect these relationships, we perturb the system by overexpressing G4-DNA helicases (DHX36 and BRIP1), treating with the G4-destabilizing agent PhpC, and knocking down the novel G4-binding protein RFC3. Our integrated analysis reveals how G4-DNA spatially and temporally regulates replication-transcription coupling, with important implications for understanding genome stability in cancer. These findings provide new insights into the role of G4-DNA as a regulatory nexus between DNA replication and gene expression.

overall_design: This study investigates the role of G4-DNA in regulating DNA replication-coupled transcription by combining cell cycle synchronization, genetic perturbations, and multi-omics profiling in HCCLM3 hepatocellular carcinoma cells. Using a double-thymidine block, we synchronize cells to Early S phase to examine phase-specific dynamics of G4-DNA structures and their interplay with transcription machinery. To dissect mechanistic relationships, we (1) overexpress G4-DNA helicases (DHX36/BRIP1), (2) treat with the G4-destabilizing agent PhpC, and (3) knockdown the novel G4-binding protein RFC3 in synchronized cells. These perturbations are analyzed through CUT&Tag (profiling transcription-associated proteins like RNA Pol II-S2P/S5P and NELF complex) and PRO-seq (quantifying transcriptional output). Our integrated approach will delineate how G4-DNA modulates replication-transcription crosstalk, with implications for understanding genome stability in cancer.

first: Xuedan

last: Sun

first: Shixiang

last: Pan

last: Zhang

first: Bo

last: Chu

first: Lianxin


title: Amyloid-β driven Alzheimer’s disease reshapes the colonic immune system in mice.

city: Novato

first: Dan

last: Winer

state: CA

address: 8001 Redwood Blvd, Novato, CA 94945

institute: Buck Institute for Research on Aging

summary: The “gut-brain axis” is an emerging target in Alzheimer’s disease (AD), though its immunological features remain poorly understood. Using single-cell RNA sequencing, coupled to extensive spectral-tuning flow cytometry validation of the colon immune compartment in the 5XFAD amyloid-β mouse model, we found several AD-associated changes including in B/plasma cell activity. Notably, levels of CXCR4+ antibody-secreting cells are reduced in 5XFAD colons. This change corresponds with accumulating CXCR4+ B cells and gut-specific IgA+ cells in the brain and dura mater, respectively. Consistently, a chemokine ligand for CXCR4, CXCL12, is expressed at higher levels in the 5XFAD brain and in in silico analyzed human AD brain studies, supporting altered neuroimmune trafficking. An inulin prebiotic fiber diet could expand gut IgA+ cells, rescue peripheral Treg levels, reduce dysbiosis, improve serum microbial metabolite levels and attenuate overall AD-associated frailty. Our study reveals key aspects of the gut-brain axis and highlights potential targets against AD.

overall_design: 16s rRNA sequencing data of stool samples taken from 5xFAD and WT mice fed control, inulin, or high fat diets.

first: Priya

last: Makhijani

first: Max

last: Manwaring-Mueller


title: Immune Receptor Lag3 Deletion Alleviates Neurodegeneration Phenotypes in a Mouse Model of Alzheimer’s Disease

city: Research Triangle Park

first: Elizabeta

last: Gjoneska

state: North Carolina

address: 111 TW Alexander Dr., David P Rall Building A030

department: Neurobiology Laboratory

institute: National Institute of Environmental Health Sciences (NIEHS/NIH)

summary: Alzheimer’s disease (AD) is the leading cause of dementia, but effective treatments remail unavailable. Using the 5xFAD familial AD mouse model, we show that deletion of the immune checkpoint receptor Lymphocyte activation gene 3 (Lag3) reduces amyloidosis, microgliosis, and neurodegeneration-related behavioral deficits. Transcriptional profiling revealed that Lag3 deletion reverses aberrant expression of disease-associated microglia (DAM) genes and decreased CD8+ T cells infiltration in the brain. These findings suggest that Lag3 regulates microglia function and may represent a potential therapeutic target for AD.

overall_design: RNA-seq was performed on FACS purified microglia isolated from hippocampal tissue of 36 mice representing four genotypes WT, 5xFAD+, Lag3-/-, and Lag3-/-; 5xFAD+. Female mice were analyzed at three ages (3-, 6-, and 9-month), with n = 3 biological replicates per group to assess genotype- and age-dependent transcriptional changes associated with Alzheimer’s disease progression and the role of Lag3 in modulating disease-associated phenotypes.

first: Juan

last: Wu

first: Andrew

last: Perl

first: Ashley

last: Brooks


title: Transcriptomic Analysis Initially Reveals Monocyte/Macrophage Activation Drives EV-A71-Induced Immune Dysregulation and Neural Injury in Severe HFMD

city: Xi'an

first: Muqi

last: Wang

state: Shaanxi

address: No.157 West Fifth Road, Xincheng District

institute: The Second Affiliated Hospital of Xi'an Jiaotong University

summary: Objective Enterovirus 71 (EV-A71) is a major pathogen of severe hand, foot and mouth disease (HFMD) in children, but the mechanism by which it develops into severe HFMD remains unclear, especially the role of macrophage-mediated immune dysregulation. Methods Macrophages infected with EV-A71 were collected for transcriptomic analysis, and were indirectly co-cultured with nerve cells to observe their inhibitory effects on nerve cells. Results High concentration of EV-A71 infected macrophage supernatant inhibited SH-SY5Y cell proliferation. ENSG00000285779, TICAM2, RPL13AP26 and HNF4G are significantly different in EV-A71 or inactivated EV-A71 infected macrophages than in control. ENSG00000264324, ENSG00000260643, ISLR2, CCR7, TENM4, INO80B-WBP1, BLOC1S5-TXNDC5 are potential genes about direct virus damage or viral RNA recognition in macrophages. GO annotation and KEGG analysis indicate that EV-A71 infection cause the changes of neural receptor-ligand binding pathway, activation of specific immunity, calcium signaling pathway, and cell aggregation. Conclusions Macrophages are activated early during EV-A71 infection, thus initiating specific immunity, which is closely related to the severe HFMD. The nerve damage pathway and calcium signaling pathway caused by EV-A71 virus infection of macrophages deserve to more attention.

overall_design: THP-1 cell-induced macrophages infected with EV-A71, inactivated EV-A71 were collected for transcriptomic analysis,and  THP-1 cell-induced macrophages were control group.

first: Meng

first: Yaping

last: Li


title: Time-resolved miRNA-mRNA integrated analysis reveals the miRNA-mRNA networks underlying plasma membrane damage-dependent senescence and DNA damage response-dependent senescence in WI-38 normal human fibroblasts

city: Okinawa

first: Yatzu

last: Chiu

address: Tancha 1919-1

country: Japan

institute: Okinawa Institute of Science and Technology

type: Non-coding RNA profiling by high throughput sequencing

summary: Cellular senescence is a stable cell cycle arrest associated with upregulated inflammatory responses. Senescent cells contribute to various pathological and physiological processes including organismal aging and cancer. Cellular senescence can be induced by various cellular stresses including DNA damage, telomere shortening, oncogene activation, and epigenetic alterations. We have shown that plasma membrane damage can also induce cellular senescence. However, common and specific molecular mechanisms among different senescent cell subtypes remain unknown. MicroRNAs (miRNAs) regulate mRNA and rewire gene expression profiles, contributing to multiple processes including cellular senescence. Here, we performed time-resolved miRNA sequencing and compared the results with mRNA sequencing results using cells experiencing plasma membrane damage-dependent senescence (PMD-Sen) and cells undergoing DNA damage response-dependent senescence (DDR-Sen).

overall_design: miRNA sequencing of proliferating and senescence-induced WI-38 cells. Two biological replicates were analyzed for each of 4 conditions (Young proliferating, SDS-treated, DXR-treated, and replicative senescence); SDS-treated and DXR-treated cells were collected at Day 0, 1, 2, 3, 4, 6, 8 and 16 after removal of SDS or DXR.

first: Yohsuke

last: Moriyama

first: Keiko

last: Kono


title: G-Quadruplex DNA suppresses Transcription during DNA Replication [PRO-Seq]

first: sun

last: xuedan

first: Xuedan

last: Liu


title: DERIVATION OF HUMAN FETAL KIDNEY ORGANOIDS MIMICKING NOTCH-DEPENDENT EPITHELIAL MATURATION AND TUBULE DEVELOPMENT [bulk RNA-Seq]

city: Ramat Gan

first: Benjamine

last: Dekel

address: Tel Hashomer

country: Israel

institute: heba Medical Center: Tel Hashomer, Tel Aviv, IL

summary: Pluripotent stem cell–derived kidney organoids (PSC-KOs) have been put forward as a preferred culture system in which to study human kidney development and disease. In contrast, the development of human fetal kidney tissue–derived organoids (hFKOs) that could serve as a benchmark for PSC-KOs has not advanced very far. Herein, utilizing a chemically defined serum-free medium, we established a long-term culture protocol for hFKOs that self-organize into polarized renal epithelium and faithfully recapitulate nephrogenic and ureteric bud cell lineages. Bulk transcriptomics, single-cell RNA sequencing, and pseudotime analysis along with immunostaining revealed diverse populations among hFKOs, with a preserved differentiation axis mostly at higher levels and to a greater extent than for PSC-KOs. Accordingly, compared to PSC-KOs, hFKOs were significantly enriched for the NOTCH signaling pathway genes, allowing single-cell analysis of changes following NOTCH inhibition. We observed a preferential increase of mature distal tubules at the expense of early proximal tubules and defined a new adaptive prominin 1–expressing (PROM1+, or CD133+) cell state that escapes NOTCH inhibition to generate proximal and distal tubules. Overall, the concomitant understanding of developmental processes using hFKOs is a key development for the fields of kidney stem cell biology and regenerative medicine.

overall_design: Characterization of human fetal kidney organoids (hFKOs) at P0 and P5-P6 and iPSC-derived kidney organoids (iPSC-KOs) for comparison via bulk RNA sequencing. P0 (3 weeks cluture) of week 18 human fetal kidney, with 3 replicates. P5 and P6 (5 months of culture) of week 18 human fetal kidney, with 4 replicates. iPSC-derived kidney organoids day 10 and 18 of Freedman et al. differentiation protocol, WTC-11 cell line, 3 replicates.

first: Michael

last: Namestnikov

first: Osnat

last: Cohen-Zontag

first: Dorit

last: Omer

first: Benjamin


title: KOLF2.1J iTF-Microglia: A standardized platform to study microglial transcriptional regulatory networks in CNS disease [RNA-seq]

city: Huntsville

first: Richard

middle: M.

last: Myers

state: AL

address: 601 Genome Way

institute: HudsonAlpha Institute for Biotechnology

summary: Understanding transcriptional regulatory networks (TRNs) in microglia is key to uncovering mechanisms driving central nervous system (CNS) disorders. Human iPSC-derived models offer a tractable system for studying microglia, yet variability between lines has limited reproducibility. Here, we use the standardized KOLF2.1J iTF line to rapidly generate microglia-like cells (iTF-Microglia) and profile TRNs under homeostatic and inflammatory conditions. iTF-Microglia closely resemble primary brain microglia at both transcriptomic and epigenomic levels. Integrative analyses reveal microglia-enriched candidate cis-regulatory elements (cCREs) and dynamic enhancer remodeling upon differentiation and LPS+IFNG stimulation, involving key transcription factors (TFs) including NF-kB, IRF, and STAT families. TRNs active in iTF-Microglia are enriched for genetic variants linked to Alzheimer’s disease and other CNS disorders. These findings establish KOLF2.1J iTF-Microglia as a reproducible and genetically tractable platform for studying human microglial gene regulation and provide mechanistic insight into how TRN remodeling may contribute to CNS disease risk.

overall_design: RNA-seq profiling of KOLF2.1J iTF-iPSCs and KOLF2.1J iTF-Microglia that were differentiated for 18 days, which were either untreated or stimulated with 100 ng/mL LPS and 20 ng/mL IFNG for 24 hours

first: Ivan

last: Rodriguez-Nunez

first: Samuel

middle: C

last: Bartley

first: Nicholas

last: Cochran

middle: M


title: KOLF2.1J iTF-Microglia: A standardized platform to study microglial transcriptional regulatory networks in CNS disease [Hi-C]

overall_design: HiC profiling of untreated KOLF2.1J iTF-iPSCs and Day 18 KOLF2.1J iTF-Microglia that were either untreated or stimulated with 100 ng/mL LPS and 20 ng/mL IFNG for 24 hours


title: Stromal Transcriptomics Uncover LIF as a Key Effector in High Tumor Budding Triple-Negative Breast Cancer

city: Bangkok

first: Pimchanok

last: Phankeaw

state: Bangkok

address: 2 Wanglang Rd., Bangkok Noi, Siriraj

department: Immunology

country: Thailand

institute: Mahidol University

summary: The overexpressed genes in FAP-positive CAFs from high TB-TNBCs included ZNF235, ANKRD30B, SLC26A2, SPDYC, CDKN1C, LIF, and FAM83A. The secreted LIF was found in 41.1% of TNBC cases with high levels detected in CAFs, while 26.2% of cases showed high LIF production in cancer cells. The recombinant LIF significantly promoted breast cancer cell migration and enhanced PD-L1 expression, effects that were attenuated by EC359. This study highlights the correlation of high TB in TNBC with poor prognosis and upregulation of key signaling pathways in CAFs. FAP-positive CAFs overexpress genes like LIF, which promotes cell migration and PD-L1 expression. LIF inhibition reduces these effects, suggesting LIF as a potential therapeutic target in TB-associated TNBC progression and immunotherapy.

overall_design: The 170 formalin-fixed paraffin-embedded TNBC tissues were assessed for TB by pan-cytokeratin immunohistochemistry (IHC). Its clinicopathological correlations were examined through univariate and multivariate analyses, with overall survival (OS) evaluated using Kaplan-Meier analysis. CAFs whole transcriptomic profiles of 13 TNBCs was conducted using Templated Oligo-Sequencing and the differential expression was analyzed in R studio with the DESeq2 package. Pathways associated with differentially expressed genes were identified using the Enrichr package. The level of leukemia inhibitory factor (LIF) was explored by IHC in 141 TNBCs, and its prognostic significance was determined. The induction of TNBC cell migration and expression of programmed death-ligand 1 (PD-L1) by a recombinant LIF, along with attenuation by EC359, a LIF inhibitor, were investigated using Transwell assay and flow cytometry.

first: Suparada

last: Khanaraksombat

first: Warapan

last: Numprasit

first: Pranisa

last: Jamjuntra

first: Punn

last: Augsornworawat

first: Malee

last: Warnnissorn

first: Peti

last: Thuwajit

first: Chanitra


title: HUMAN FETAL KIDNEY ORGANOIDS MODEL EARLY NEPHROGENESIS AND NOTCH-DRIVEN CELL FATE [scRNA-seq]

first: Benjamine

summary: Pluripotent stem cell–derived kidney organoids (PSC-KOs) are widely used to model human kidney development and disease. However, organoids from human fetal kidney tissue (hFKOs), which could benchmark PSC-KOs, remain underdeveloped. Here, using a chemically defined serum-free medium, we established a prolonged culture protocol for hFKOs that self-organize into polarized renal epithelium, reinitiate from NCAM1+ progenitors, and recapitulate nephrogenic and ureteric bud lineages. Bulk transcriptomics, single-cell RNA sequencing, pseudotime analysis, and immunostaining revealed diverse cell populations, with a preserved epithelial progenitor pool and tubular differentiation axis—both more robust than in PSC-KOs. hFKOs were enriched for NOTCH signaling genes, enabling single-cell analysis of pharmacological NOTCH inhibition. This revealed a maturation block with increased nephron progenitors and a bias toward distal over early proximal tubule fates. We also identified a novel prominin-1–expressing cell state that evades NOTCH inhibition to generate both proximal and distal tubules. Overall, hFKOs provide a developmentally faithful model and offer critical insights into kidney morphogenesis, advancing the fields of stem cell biology and regenerative medicine.

overall_design: Two samples of human fetal kidney organoids (hFKOs) at P0 after 2-3 weeks of culture, one hFKO sample derived from week 20 thawed human fetal kidney cells (hFK18) the other hFKOs sample derived from freshly dissociated week 15 of gestation human fetal kidney (hFK26).


title: KOLF2.1J iTF-Microglia: A standardized platform to study microglial transcriptional regulatory networks in CNS disease [ChIP-seq]

overall_design: ChIP-seq of H3K27ac in untreated KOLF2.1J iTF-iPSCs and Day 18 KOLF2.1J iTF-Microglia that were either untreated or stimulated with 100 ng/mL LPS and 20 ng/mL IFNG for 24 hours


title: HUMAN FETAL KIDNEY ORGANOIDS MODEL EARLY NEPHROGENESIS AND NOTCH-DRIVEN CELL FATE [scRNA-Seq 2]

overall_design: Two samples of human fetal kidney organoids (hFKOs) at P0 after 2-3 weeks of culture, one hFKO sample is treated with the γ-secretase inhibitor DAPT the other hFKOs sample is treated with DMSO, serves as a control. hFKOs were derived from freshly dissociated week 20 human fetal kidney. NOTCH inhibition in hFKOs: After 3 days of initial culture, DAPT, reconstituted in DMSO, was added to the culture medium at 5 uM final concentration; this medium was refreshed every 2 days. hFKOs were grown for 2–3 weeks under NOTCH inhibition next to control wells in which the culture medium was supplemented with DMSO only.

first: Michael


title: KOLF2.1J iTF-Microglia: A standardized platform to study microglial transcriptional regulatory networks in CNS disease [ATAC-seq]

overall_design: ATAC-seq profiling of untreated KOLF2.1J iTF-iPSCs and Day 18 KOLF2.1J iTF-Microglia that were either untreated or stimulated with 100 ng/mL LPS and 20 ng/mL IFNG for 24 hours


title: Hand1 gene replacement with Hand2 reveals overlap in function with unique occurrence of omphalocele and heart defects

city: Bloomington

first: Center for Genomics and Bioinformatics

last: IU

state: IN

address: 1001 E Third St

department: Biology

institute: Center for Genomics and Bioinformatics

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

overall_design: Refer to individual Series


title: An interpretable and adaptive autoencoder for efficient tissue deconvolution

city: Pamplona

first: Mikel

last: Hernaez

state: Navarra

address: Avda. Pío XII, 55

department: Bioinformatics

country: Spain

institute: CIMA (Centre for Applied Medical Research)

summary: Deconvolution models are a powerful tool for extracting cell type-specific information from bulk gene expression profiles. Current methods leverage advanced machine learning models and high-resolution sequencing, like single-cell RNA-sequencing (scRNA-seq), showing promising results across diverese tissues and conditions. However, they still present important limitations: Many depend on selecting a robust reference, which can strongly affect the deconvolution. Secondly, pseudobulk data used for training and real bulk RNA-seq samples often exhibit strong distribution shifts, which are currently unaccounted for. Finally, most deconvolution approaches behave as black boxes, which can compromise the reliability of the results. Here, we present Sweetwater, an adaptive and interpretable autoencoder that efficiently deconvolves bulk samples leveraging multiple classes of reference data. Moreover, we propose an improved way of generating training data from a mixture of FACS-sorted FASTQ files, reducing platform-specific biases and outperforming current single-cell-based references. Furthermore, we introduce a gold standard dataset to facilitate fair and accurate evaluation of deconvolution approaches. Finally, we demonstrate that Sweetwater adapts effectively to deconvolved samples during training, uncovering biologically meaningful patterns and enhancing result's reliability. Sweetwater is available at https://github.com/ML4BM-Lab/Sweetwater, and we anticipate it will expedite the accurate examination of high-throughput clinical data across diverse applications.

overall_design: This dataset was developed to benchmark cell type deconvolution methods using both single-cell and bulk RNA sequencing data from peripheral blood immune cells. Four immune cell types—T cells, B cells, Neutrophils, and Monocytes—were FACS-isolated from human PBMCs, and bulk RNA-seq was performed on each purified population. To generate controlled mixtures with known composition, seven artificial mixes were created by manually combining RNA from the four purified cell types in specific proportions, and each mix was prepared in duplicate (e.g., Mix 1.1 and Mix 1.2). The mixtures were composed as follows: Mix 1.1 and 1.2 consisted of 25% Neutrophils, 25% T cells, 25% B cells, and 25% Monocytes; Mix 2.1 and 2.2 contained 30% Neutrophils, 30% T cells, 10% B cells, and 30% Monocytes; Mix 3.1 and 3.2 included 50% Neutrophils, 20% T cells, 10% B cells, and 20% Monocytes; Mix 4.1 and 4.2 were composed of 47% Neutrophils, 47% T cells, 6% B cells, and 0% Monocytes; Mix 5.1 contained 50% Neutrophils, 49% T cells, 1% B cells, and 0% Monocytes, while Mix 5.2 had 50% Neutrophils, 35% T cells, 1% B cells, and 14% Monocytes; Mix 6.1 and 6.2 were made up of 25% Neutrophils, 25% T cells, 0% B cells, and 50% Monocytes; and Mix 7.1 and 7.2 included 50% Neutrophils, 50% T cells, and 0% of both B cells and Monocytes. This experimental design allows for the controlled testing of deconvolution methods under varying levels of cell type abundance, including rare cell type scenarios and highly imbalanced compositions, providing a robust benchmark framework.

first: Jesus

last: de la Fuente

first: Naroa

last: Legarra-Marcos

first: Aintzane

last: Diaz-Mazkiaran

first: Guillermo

last: Serrano

first: Irene

last: Marin-Goñi

first: Markel

last: Benito-Sendin

first: Ana

last: García Osta

first: Krishna

middle: R

last: Kalari

first: Carlos

last: Fernandez-Granda

first: Idoia

last: Ochoa


title: Targeting AXL can effectively inhibit c-Met-induced therapeutic resistance in renal cancer

city: Boston

first: Marc

last: Machaalani

state: MA

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: The mechanism(s) for therapeutic resistance against c-Met/receptor tyrosine kinase (RTK) inhibitor(s) in renal cancer is totally unexplored. In renal cell carcinoma (RCC) cells, both AXL and c-Met are highly overexpressed and they form a complex. Interestingly, the prolonged treatment with c-Met/RTK inhibitor, Cabozantinib (Cabo), which is being used for the treatment of RCC patients, markedly increased the level of total c-Met and promoted renal cancer cell proliferation. This effect was confirmed not only in vitro but also in murine models and renal tumor tissues from Cabo-treated patients. Also, the lower concentrations of Cabo treatment could not inhibit HGF (c-Met ligand)-induced c-Met phosphorylation; rather they further increased the phosphorylation of the receptor and promoted downstream signaling events for tumor growth. In addition, our findings indicate that Cabo treatment induces AXL-c-Met association, and it interferes with the physiological degradation processes of c-Met within renal cancer cells. However, either the inhibition or the knockout of AXL could significantly overcome the therapeutic resistance against c-Met inhibitor(s); and it markedly induced apoptotic cell death through increased oxidative stress and inhibition of the transcription factor, Nrf2. We generated Cabo-resistant RCC cells, and we observed that the expression of both c-Met and AXL are markedly overexpressed in these cells; and the inhibition of AXL (through TP-0903) can   resensitize the cancer cells to Cabo-mediated cell death. Moreover, we found significant differences in the epigenomic profile of the Cabo-resistant RCC cells compared with Cabo-sensitive cancer cells. Our in-depth studies suggest that AXL plays a major role in mediating therapeutic resistance against c-Met inhibitor(s). A combination therapy using c-Met inhibitor(s) in the presence of an AXL inhibitor can play a pivotal role to overcome acquired resistance against RTK inhibitors in renal cancer.

overall_design: RNA-seq and ChIP-seq of the histone modifcation H3K27ac were performed in cabozantinib-sensitive and cabozantinib-resistant renal cell carcinoma cell lines

first: Akash

last: Sabarwal

first: Soumitro

last: Pal

first: Eddy

last: Saad

first: Karl

last: Semaan

last: Eid

first: Toni

last: Choueiri


title: Origin and Correlates of Viral Rebound in SIV-Infected Rhesus Macaques Following ART Discontinuation

first: Dan

last: Barouch

address: 3 Blackfan Cir

department: CVVR

institute: Beth Israel Deaconess Medical Center

summary: The earliest events of viral rebound following discontinuation of ART in persons living with HIV-1 (PLWH) remain largely unknown. Here we show that viral rebound in SIV-infected rhesus macaques following ART discontinuation involves serial clonal reactivation in gastrointestinal (GI) and lymph node (LN) tissues followed by rapid local and systemic spread. We investigated viral rebound dynamics in 18 SIV-infected rhesus macaques treated with antiretroviral therapy (ART) for 70 weeks and necropsied on day 12  after ART discontinuation. Using molecularly barcoded SIVmac239M, we tracked viral clonotypes following ATI in both peripheral blood and necropsy tissues. Viral rebound originated by reactivation of a single or a few clonotypes from a limited number of GI tissues and deep LNs, followed by replication of each clonotype and then serial reactivation of additional clonotypes from different anatomic sites, resulting in oligoclonal plasma viremia. Daily transcriptomic and proteomics profiling in peripheral blood identified early upregulation of pathways related to T cell signaling, cytokine responses, and cellular metabolism prior to detectable plasma viremia, presumably reflecting initial viral replication in tissues. Taken together, these data demonstrate the early clonal dynamics of viral rebound in SIV-infected macaques following ART discontinuation, which provides critical information for the development of next generation HIV-1 cure strategies.

overall_design: 18 outbred, Indian-origin adult male and female rhesus macaques (Macaca mulatta) (n = 6/group) were intravenously infected with 5,000 infectious units (IUs) of molecularly barcoded SIVmac239M7 and initiated ART on Day 6, Day 9, or Day 12 following infection. The ART regimen consisted of daily subcutaneous injections of a pre-formulated cocktail of tenofovir disoproxil fumarate (TDF; 5.1 mg/mL), emtricitabine (FTC; 40 mg/mL), and dolutegravir (DTG; 2.5 mg/mL). Animals were treated with daily ART for 70 weeks, and plasma and cell-associated SIV DNA (CA-DNA) and RNA (CA-RNA) was monitored longitudinally.

first: Irena

middle: V

last: King

first: Malika

last: Aid

first: Alessandro

last: Colarusso

first: Victoria

middle: E

last: Walker-Sperling

first: Erica

middle: N

last: Borducchi

first: Romas

last: Geleziunas

first: Louis

middle: J

last: Picker

first: Jeffrey

middle: D

last: Lifson

first: Brandon

middle: F

last: Keele

middle: H


title: Development of an in vitro method to assess the immunogenicity of biologics in the prevention of infectious diseases

city: Warsaw

first: Monika

middle: Maria

last: Staniszewska

address: Poleczki 19

department: CEZAMAT

country: Poland

institute: Warsaw University of Technology

summary: We present a series of preclinical studies focused on developing in vitro 2D and 3D models for assessing immunogenic factors in preventing infectious diseases. Human peripheral blood mononuclear cells (PBMC) and Calu-3 cell lines (bronchial epithelial cells) were used to develop 2D and 3D models. Peptides: Spike-S1-His (S-His), nucleocapsid-His and adjuvants: human adenovirus five serotype-based viral vector (AdV-D24-ICOSL-CD40L), armed with inducible co-stimulator (ICOSL) and CD40 ligand (CD40L), and a vector lacking these transgenes (AdV5/3) were used due to their effective initial interaction with antigen-presenting cells (APC). Studying the potency of biologics in vitro revealed a significant increase in the percentage of CD4+ TCM, CD4+ TEMRA, and CD4+ TEM lymphocyte subpopulations involved in memory cell generation after 24 hours of treatment. Prolonging the exposure for 7 days, a significant increase in CD4+ cells was observed when PBMCs were treated with AdV1 (56.00 ± 0.26% vs. 48.17 ± 1.10%). In contrast, a decrease in CD8+ cells was observed in those treated with AdV1 (37.93 ± 0.35%) compared to AdV1+S-His+N-His (38.47 ± 0.38%) versus the untreated group (44.63 ± 1.07%). A decrease in EMRA was noted when PBMCs were treated with AdV1+S-His+N-His (2.97 ± 0.23% vs. 4.50 ± 0.35%). Moreover, it was pointed out that PBMCs treated with AdV1 alone or in combination with S-His and N-His showed an elevated number of naïve CD4+/CD8+ and SCM CD4+/CD8+ cells. No changes in the number of EMRA CD4+ subpopulations were detected when PBMCs were treated with AdV2 compared with untreated ones (4.27 ± 0.06% vs. 4.50 ± 0.35%). Analysis of the humoral response induced by AdV1, AdV2, S-His, N-His, AdV1+S-His+N-His, and AdV2+S-His+N-His showed that AdV1 alone (4.17 ± 0.25% vs. 3.17 ± 0.06%) and in combination with S-His and N-His (3.87 ± 0.25 vs. 3.17 ± 0.06%) slightly increased the number of CD19+ cells. RNA-Seq analysis of PBMC cells in the 3D model revealed gene overexpression, including FGFR4, associated with the Rap1 pathway in samples exposed to AdV1+S-His+N-His. Thus, the proposed platform's impact on lymphocyte differentiation was confirmed, and cytokine profile analysis in this sample revealed elevated levels of IL-10, IL-12p70, and IL-8. All samples exposed to AdV showed increased levels of IFN-γ. The safety and biodistribution studies of the vaccine platform demonstrated that a 30-day exposure did not impact mice's survival or organ morphology. Exploring the CD40 pathway notably reveals its significant impact on immune cell populations, suggesting potential therapeutic avenues.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for PBMC and Calu-3 cells untreated and treated with AdV1 (100 VP/mL), S-His, and N-His.

first: Joanna

last: Baran

first: Łukasz

last: Kuryk

first: Mariangela

last: Garofalo

first: Marta

last: Prygiel

first: Aleksandra

last: Zasada

first: Teresa

last: Szczepińska

first: Anna

first: Deepak

last: Kala

first: Piotr

last: Majewski

first: Radowsław

last: Charkiewicz


title: PD-L1⁺ Neutrophils Mediate Immune Regulation of CD8⁺ T Cells in Halo Nevi

city: Suzhou

first: Yixuan

last: Zhang

address: No.9 Chongwen Road

institute: Suzhou University

summary: Halo nevi are clinically common and are characterized by a circle of leukoderma around the central melanocytic nevus. Studies have shown that the pathogenesis of the surrounding leukoderma is similar to that of vitiligo and is associated with the role of CD8⁺ T lymphocytes in melanocyte destruction. Notably, some halo nevi exhibit a tendency for spontaneous regression of the surrounding leukoderma, yet the underlying mechanisms remain unclear. Furthermore, histopathological findings have revealed neutrophil infiltration in halo nevi, but the specific immune mechanisms involving neutrophils have not been thoroughly investigated. This study investigated the role of neutrophils in halo nevi through histopathological and immunological analyses, aiming to provide some clues for identifying the mechanisms underlying the regression of surrounding leukoderma. We examined the infiltration patterns of immune cells in halo nevi, with a particular focus on IFN-γ-induced PD-L1 expression in neutrophils and its potential immunoregulatory effects. The results demonstrated that IFN-γ expression in the lesional skin of halo nevi contributed to the induction of PD-L1 expression in neutrophils. PD-L1⁺ neutrophils promoted apoptosis and suppressed the function of CD8⁺ T lymphocytes. This regulatory mechanism influences the local immune response and may facilitate the repigmentation of the surrounding leukoderma. This study is the first to explore the involvement mechanism of neutrophils in halo nevi and to reveal the potential immunoregulatory role of PD-L1. The elucidation of this mechanism not only provides a more comprehensive understanding of autoimmune skin diseases but may also offer new strategies for targeted therapy in related pigmentary disorders, such as vitiligo.

overall_design: Neutrophils were collected from both the IFN-γ-stimulated group (Neutrophils were stimulated with IFN-γ at a concentration of 10 ng/mL for 24 hours) and the unstimulated group.

first: Yingying

last: Xu

first: Wenjun

last: Cui

first: Min

last: Li

first: Lu

last: Liu


title: Vaccination against Onchocerca volvulus induces IgG-mediated protective immunity dependent on neutrophils and complement

city: Philadelphia

first: Nathan

last: Ryan

institute: Thomas Jefferson University

summary: Onchocerciasis remains a significant cause of morbidity and economic loss in sub-Saharan Africa. Despite the existence of effective therapeutics, a prophylactic vaccine targeting the etiologic agent, Onchocerca volvulus, is needed to control ongoing disease and transmission. Mice were vaccinated against O. volvulus with a fusion of the recombinant antigens Ov-103 and Ov-RAL-2 (Ov-FUS-1) with Advax-CpG adjuvant. Immunized mice developed protective immunity with the killing of third-stage larvae (L3) within 36 hours of challenge infection. IgG from immunized mice passively transferred protective immunity to naïve mice, indicating that antigen-specific IgG mediated parasite elimination. Neutrophils were the most abundant subset of immune cells recruited to the parasite microenvironment in vivo, and their depletion resulted in the total loss of immune-mediated larval killing. Analysis of neutrophil gene expression revealed that both vaccination and the presence of O. volvulus larvae were capable of modulating neutrophil transcriptional activity. The mechanism by which antigen-specific IgG and neutrophils collaborated to kill L3 was independent of Fcγ receptors. However, the elimination of complement component C3 prevented vaccine-induced protection, which suggests these components may interact through the complement system. This study describes a vaccine-induced mechanism of protective immunity against O. volvulus L3 dependent on IgG, neutrophils, and complement, highlighting an effective collaboration between the innate and adaptive arms of the immune system to control O. volvulus infection.

overall_design: Samples were 95-99% pure neutrophil populations collected from diffusion chambers that were implanted subcutaneously into either immunized or control mice. Samples were collected 18 or 36 hours post implantation. Diffusion chambers were implanted either with or without O. volvulus L3.

first: Jessica

middle: A

last: Hess

first: Mohini

last: Nakhale

first: Annabel

last: Ferguson

first: Darrick

last: Carter

first: Sara

last: Lustigman

first: David

last: Abraham


title: Hand-powered interfacial electric-field-enhanced water disinfection system

first: zhidi

last: chen

state: 广东省

address: 深圳市南山区创新科技中心T4 1405

institute: 深圳大学

summary: Mechanical energy–driven portable water disinfection has attracted attention for its electricity-free operation, but this approach generally faces bottlenecks such as a high mechanical activation threshold, energy dispersion, and low interfacial reaction efficiency, making it difficult to achieve rapid and stable pathogen inactivation in practical scenarios. Here we report a manually operated portable water disinfection system that can inactivate 99.9999% of V. cholerae within 1 minute and demonstrate broad-spectrum disinfection against bacteria, fungi, parasites, and viruses. Amino-modified SiO₂ nanoparticles loaded with Au nanoparticles capture hydrated electrons and transfer them to the electret surface to generate localized nanoscale electric fields, which are further strengthened by hydrophobic  fluorinated groups. This interfacial architecture not only promotes charge accumulation and transfer, but also leverages the intensified electric field to actively drive reactive oxygen species (ROS) generation at the solid–liquid–air interface, thereby markedly enhancing disinfection rate and efficacy compared with existing contact electrification–based disinfection technologies. Owing to its ease of operation, ourinterfacial electric-field-enhanced (IEFE) disinfection system is readily deployable in disaster relief and resource-constrained regions.

overall_design: This study aimed to investigate transcriptomic changes in Escherichia coli induced by interfacial electric-field-enhanced (IEFE) disinfection using SiO2@NF_Au nanostructures. Bacterial cultures were grown to mid-log phase and divided into two groups: untreated controls and samples subjected to IEFE treatment for 1 min. Each group contained three independent biological replicates. Total RNA was extracted from bacterial cells, and rRNA was removed prior to library preparation. Strand-specific RNA-seq libraries were constructed using a TruSeq Stranded Total RNA Library Prep Kit and sequenced on an Illumina platform. Comparative transcriptome analysis was performed to identify differentially expressed genes and associated biological pathways.

first: Zhidi

last: Chen

first: Yajing

first: Panjing

last: Lv


title: Exome sequencing reveals the genetic architecture of non-syndromic orofacial clefts and identifies BOC as a novel causal gene

city: 咸阳市

first: qing

last: he

state: 陕西省

address: 钓台街道西安交大创新港21号楼

institute: xi'an jiaotong university

summary: Nonsyndromic orofacial clefts (NSOFCs) are the most common human craniofacial defects. Genetic factors play a critical role in the pathogenesis of NSOFCs. However, known causal genes only explain a minority of the estimated heritability. The findings substantiate the genetic and allelic heterogeneity of NSOFCs and underscore the crucial role of dysregulation of OFC-related signaling pathways in the occurrence of NSOFCs. Besides, the candidate variants discovered provide a fruitful resource for further genetic studies. Particularly, three BOC missense variants (p.R407W, p.G436S and p.D1018N) are identified in three cases with cleft palate. In parallel, a BOC nonsense variant (p.R681X), co-segregating with a GLI2 missense variant (p.A543G), is identified in a multiplex family with microform cleft lip. Functional studies demonstrate while the four BOC variants are hypomorphic alleles, the GLI2 variant is a hypermorphic allele. The counteraction between BOC p.R681X allele and GLI2 p.A543G allele is likely to account for the mild phenotype in the multiplex family. Thus, this study establishes BOC as a novel causal gene and implicates a two-locus model of inheritance via the epistatic antagonism of two SHH pathway variants in NSOFCs.

overall_design: We divided the collected zebrafish embryos into two groups and performed microinjections with GLI2-WT mRNA and GLI2-A543G mRNA, respectively. After allowing the embryos to develop for 24 hours, we lysed them and extracted RNA from both groups. RNA sequencing was then performed, followed by a series of data analyses.

first: Qing

last: He

first: Huaxiang

last: Zhao

first: Yi

last: Ding


title: TDP-43 dysregulation impairs cholesterol metabolism linked with myelination defects

city: Madrid

first: Silvia

last: Corrochano

address: Calle del Prof Martín Lagos

department: Neurología

institute: Instituto de Investigación Sanitaria del Hospital Clínico San Carlos

summary: TDP-43 is a nuclear protein encoded by the TARDBP gene, which forms pathological aggregates in various neurodegenerative diseases, collectively known as TDP-43 proteinopathies, including amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). These diseases are characterized by multiple pathological mechanisms, with disruptions in lipid regulatory pathways emerging as a critical factor. However, the role of TDP-43 in the regulation of the brain lipid homeostasis and the potential connection of TDP-43 dysfunction to myelin alterations in TDP-43 proteionopathies remain poorly understood, despite the fact that lipids, particularly cholesterol, comprise nearly 70% of myelin. To investigate the causal relationship between TDP-43 dysfunction and disruptions in brain cholesterol homeostasis, we conducted multi-omics analyses (lipidomics, transcriptomics, and functional splicing) on the frontal cortex from the TardbpM323K/M323K knock-in mouse model. Lipidomic analysis revealed alterations in lipid pathways related to membrane composition and lipid droplet accumulation, particularly affecting cholesterol-related species. We found higher lipid droplets accumulation in primary fibroblast derived from these mice, as well as in the brain of the mutant mice. Similarly, the immunohistochemical detection of a lipid droplet marker was higher in the post-mortem frontal cortex, gray and white matter, of FTLD-TDP patients compared to non-neurological controls. Transcriptomic analyses showed that TDP-43 pathology led to transcriptional dysregulation of genes essential for myelin production and maintenance. We identified impaired cholesterol metabolism, mainly through the downregulation of endogenous cholesterol synthesis, alongside upregulated cholesterol transport pathways, which we further replicated in FTLD-TDP patients transcriptomic datasets. Collectively, our findings suggest that TDP-43 dysfunction disrupts brain cholesterol homeostasis, potentially compromising myelin integrity.

overall_design: Bulk RNA sequencing data from the physiological knock-in mouse model carrying the pathogenic TDP-43 M323K mutation from the frontal cortex from wild type (n=4)and homozygous (n=4) male mice at 9 months of age

first: Irene

last: García-Toledo

first: Juan M.

last: Godoy-Corchuelo

first: Luis C.

last: Fernández-Beltrán


title: Effect of subchronic ototoxic (streptomycin) exposure on the vestibular epithelium of the rat

city: Hospitalet de Llobregat

first: Jordi

last: Llorens

state: Catalunya

address: Feixa Llarga s/n

department: Ciències Fisiològiques

institute: Universitat de Barcelona

summary: Several compounds cause auditory and vestibular toxicity by targeting the sensory transducing cells of the inner ear, the hair cells (HC). These compounds, known as ototoxic compounds, may cause vestibular HC apoptosis following high dose acute exposure. However, chronic exposure to low doses has been observed to cause progressive damage. Thus, chronic ototoxic stress first cause detachment and uncoupling of the HC and their post-synaptic neurons, followed by changes in cell shape including stereocilia fusion and ending with extrusion of the HCs from the sensory epithelium towards the luminal spaces of the vestibule. The molecular mechanisms driving these phenomena have not been established. We hypothesized that this response of the vestibular epithelium to chronic ototoxic stress must include specific gene expression responses. The present SubSeries is part of a SuperSeries aimed at identifying these expression responses. Two species, two ototoxic compounds and different times were studied as a strategy to identify the most relevant responses. In the present SubSeries, the expression response of the vestibular epithelium is studied in rats exposed to streptomycin.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from vestibular epithelia of control rats and rats after subchronic ototoxic (streptomycin) exposure.

first: Alberto

last: Maroto

first: Marta

last: Gut

first: Anna

last: Esteve-Codina

first: Beatriz

last: Martín-Mur

first: Alejandro

last: Barrallo-Gimeno


title: Effect of subchronic (4 weeks) ototoxic (3,3'-iminodipropionitrile - IDPN) exposure on the vestibular epithelium of the rat

summary: Several compounds cause auditory and vestibular toxicity by targeting the sensory transducing cells of the inner ear, the hair cells (HC). These compounds, known as ototoxic compounds, may cause vestibular HC apoptosis following high dose acute exposure. However, chronic exposure to low doses has been observed to cause progressive damage. Thus, chronic ototoxic stress first cause detachment and uncoupling of the HC and their post-synaptic neurons, followed by changes in cell shape including stereocilia fusion and ending with extrusion of the HCs from the sensory epithelium towards the luminal spaces of the vestibule. The molecular mechanisms driving these phenomena have not been established. We hypothesized that this response of the vestibular epithelium to chronic ototoxic stress must include specific gene expression responses. The present SubSeries is part of a SuperSeries aimed at identifying these expression responses. Two species, two ototoxic compounds and different times were studied as a strategy to identify the most relevant responses. In the present SubSeries, the expression response of the vestibular epithelium is studied in rats exposed to 3,3'-iminodipropionitrile (IDPN) for 4 weeks.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from vestibular epithelia of control rats and rats after subchronic (4 weeks) ototoxic (3,3'-iminodipropionitrile, IDPN) exposure.


title: Effect of subchronic ototoxic (3,3'-iminodipropionitrile - IDPN) exposure on the vestibular epithelium of the mouse

summary: Several compounds cause auditory and vestibular toxicity by targeting the sensory transducing cells of the inner ear, the hair cells (HC). These compounds, known as ototoxic compounds, may cause vestibular HC apoptosis following high dose acute exposure. However, chronic exposure to low doses has been observed to cause progressive damage. Thus, chronic ototoxic stress first cause detachment and uncoupling of the HC and their post-synaptic neurons, followed by changes in cell shape including stereocilia fusion and ending with extrusion of the HCs from the sensory epithelium towards the luminal spaces of the vestibule. The molecular mechanisms driving these phenomena have not been established. We hypothesized that this response of the vestibular epithelium to chronic ototoxic stress must include specific gene expression responses. The present SubSeries is part of a SuperSeries aimed at identifying these expression responses. Two species, two ototoxic compounds and different times were studied as a strategy to identify the most relevant responses. In the present SubSeries, the expression response of the vestibular epithelium is studied in mice exposed to 3,3'-iminodipropionitrile (IDPN).

overall_design: Comparative gene expression profiling analysis of RNA-seq data from vestibular epithelia of control mice and mice after subchronic ototoxic (3,3'-iminodipropionitrile, IDPN) exposure.

first: Erin

last: Greguske


title: Effect of subchronic ototoxic exposure on the vestibular epithelium

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus


title: Microglia-astrocyte crosstalk regulates synapse remodeling via Wnt signaling

city: Worcester

first: Travis

middle: E.

last: Faust

address: 366 Plantation Street

department: Neurobiology

institute: University of Massachusetts Chan Medical School

summary: Unilateral whisker lesioning at age P4 leads to removal of thalamocortical synapses in layer IV of the barrel cortex over the course of the next 6 days. Synapse removal is mediated by microglia and induced by CX3CL1-CX3CR1 signaling between neurons and microglia. Downstream of CX3CL1-CX3CR1 activation, microglia induce astrocyte morphological changes and activation of canonical Wnt signaling in astrocytes. To explore the spatial pattern of microglia Wnt ligand expression and astrocyte Wnt receptor expression in astrocytes, we analyzed coronal sections containing the barrel cortex from 4 wild-type mice and 4 CX3CL1 knockout mice at 24 hours after whisker lesioning by multiplexed error-robust fluorescent in situ hybridization (MERFISH).

overall_design: Brains were isolated from P5 mice at 24 hours after unilteral whisker lesioning of the right side of the mouse's snout at age P4. Brains were extracted and embedded in OCT for sectioning onto specialized coverslips. Coronal sections containing the barrel cortex were collected for analysis by MERFISH. Each coverslip contained 1 coronal section from a wild-type mouse and 1 coronal section from a CX3CL1 knockout mouse.

first: Margaret

last: Boyle

first: Violeta

last: Durán-Laforet

first: Loris

middle: L

last: Ferrari

first: Robert

last: Murphy

first: Dorothy

middle: P

last: Schafer


title: Hand1 gene replacement with Hand2 reveals overlap in function with unique occurrence of omphalocele and heart defects [Spatial Transcriptomics]

first: Center for Genomics and Bioinformatics

last: IU

summary: The bHLH transcription factors HAND1 and HAND2 are expressed in partially overlapping patterns during development. Studies have established evidence for significant functional redundancy between HAND1 and HAND2. To test redundancy fully, we engineered a Hand1 allele where we directly replace the exons and intron with those of Hand2. Results show that 2% of Hand1Hand2/ Hand2 mice are viable, and fertile. The remaining Hand1Hand2/Hand2 embryos exhibit neonatal lethality due to omphalocele, ventricular septal defects and conduction anomalies. Omphalocele can occur due to altered gut rotation and transcriptomic expression analysis reveals that established gene expression patterns associated with normal gut rotation are compromised. Interrogation of cardiac function in surviving Hand1Hand2/Hand2 mice reveals QRS abnormalities and accompanies cardiac morphogenic defects. These data support previous findings that HAND factors exhibit extensive functional overlap but do reveal that unique functions for HAND1 and HAND2 proteins within the Hand1 expression domain that are required for normal embryonic development.

overall_design: Four Control E13.5 day embryos that were sectioned transverse  at the level of the umbilicus and four Hand1^Hand2/Hand2 E13.5 day embryos that were sectioned transverse  at the level of the umbilicus were transferred onto Visisum slides (10X Genomics) with 11mm capture area with 55 um diameter "spots" using a CytAssist (10X genomics). Four to six sections depending on the individual emrbyo were transfered to both the A side and B side of a single slide yeilding 8 to 12 section replicates per sample. The A side of one of the Hand1^Hand2/Hand2 Mutants (V52L19-098_A1) failed and was not included in this study.

first: Anthony

middle: B

last: Firulli

first: Beth

first: Ram

last: Podicheti

first: Douglas

last: Rusch


title: Distinct classes of 21 and 24-nt phasiRNAs suggests diverse mechanisms of biogenesis and function in rice anther development

city: Davis

first: Patricia

last: Baldrich Gonzalez

address: 451 Health Sciences Dr., Davis, CA 95616

department: Genome Center

institute: University of California - Davis

summary: PhasiRNAs (phased small interfering RNAs) are a major class of plant small RNAs known to be key regulators in male reproductive development of maize and rice (Oryza sativa), among other plants. Earlier research focused primarily on premeiotic 21-nt phasiRNAs and meiotic 24-nt phasiRNAs, while new studies uncovered a premeiotic class of 24-nt phasiRNAs. The biogenesis and function of these phasiRNAs remains unclear. We conducted an integrative analysis combining small RNA sequencing and transcriptomic profiling of small RNA-associated genes across Kitaake rice anther developmental stages to map associations between sRNA-related genes and phasiRNA classes. We identified new classes of postmeiotic 21-nucleotide and postmeiotic 24-nucleotide phasiRNA-producing loci and characterized their unique accumulation patterns. Our findings reveal distinct differences in nucleotide composition and register accumulation among the phasiRNA classes, suggesting the presence of diverse mechanisms of biogenesis and function. Our results provide new insights into the regulatory complexity of phasiRNAs, establishing a foundation for further functional studies and advancing our understanding of their roles in anther development and their underlying mechanisms.

overall_design: Anthers of rice WT kitaake plants at 10 different sizes (0.4mm, 0.6mm, 0.8mm, 1.0mm, 1.2mm, 1.4mm, 1.6mm, 1.8mm, 2.0mm, and 2.5mm) were collected. For each anther size there were 3 biological replicates.

first: Rachel

last: Jouni

first: Caroline

last: Henry

first: Blake

last: Meyers

last: Baldrich


title: The scRNA-seq analysis of immune cells in colorectal cancer liver metastatic lesions formed by MC38-LM3b-shScramble and MC38-LM3b-shSLAMF3.

city: chengdu

first: Shufang

last: Liang

state: State...

address: chengdu

institute: sichuan university

summary: MC38-LM3b-shScramble and MC38-LM3b-shSLAMF3 liver metastatic lesions formed by spleen injection were used to isolate immune cells with CD45 magnetic beads, followed by scRNA-seq sequencing to analyze the effect of SLAMF3 on the colorectal cancer liver metastatic microenvironment.

overall_design: Liver metastatic lesions were formed in mice with MC38-LM3b-shScramble and MC38-LM3b-shSLAMF3. For each group, liver metastatic lesions from three mice were pooled together for subsequent CD45-positive immune cell sorting and scRNA-seq analysis.

first: Yinheng

last: Luo


title: The Molecular Mechanism of Ambrosin Induced Toxicity of Breast Cancer and Bladder Cancer Cells

city: Ann Arbor

first: Brian

last: Magnuson

state: MI

address: 1500 East Medical Center Drive

institute: University of Michigan

summary: Sesquiterpene lactones (STL) are lipophilic compounds synthesized as secondary metabolites in species across the plant kingdom, most notably in the family Asteraceae. One STL, found in North African Ambrosia maritima (A. maritima), and Caribbean Ambrosia hispida (A. hispida), is the compound ambrosin. Ambrosin exhibits several desirable pharmacologic characteristics, including compliance with the Rule of Five (RO5) pharmacokinetic profile. We have extracted ambrosin from A. maritima and A. hispida and demonstrated its cytotoxicity in bladder cancer and breast cancer cell lines in low micromolar ranges. Ambrosin also inhibited cancer stem cells and secondary spheroid formation of multiple bladder cancer and breast cancer cell lines. RNA Bru-Seq of ambrosin treated bladder cancer and breast cancer cells revealed a mitochondrial apoptotic gene signature as well as activation of glutathione metabolism, indicating the generation of reactive oxygen species (ROS). RNA Bru-Sequencing and drug target mapping also revealed potential antagonistic activity of ambrosin against the EGFR tyrosine kinase and Rho/Rac GTPases. Further studies showed that ambrosin inhibited EGFR auto-phosphorylation at tyrosine 1068 (Y1068) as well as the inhibition of Cdc42 GTPase and RhoC GTPase activity. These findings indicate novel mechanisms of action and justify further considerations for ambrosin pharmaco-development as a potential chemotherapeutic agent for advanced bladder cancer and triple negative breast cancer.

overall_design: Two bladder cancer cell lines (UMUC5 and UMUC9) and two breast cancer cell lines (BT20 and MDA231) were treated with vehicle (Veh) or ambrosin (Amb) for 4h prior to harvest. Bromouridine labeling was performed 30 min prior to harvest for nascent RNA sequencing (Bru-seq).  Three replicates per condition were produced for a total of 24 samples.

first: Layla

last: El-Sawy

first: John

last: Rubin

first: Luke

last: Broses

first: Christopher

last: Patsalis

first: Marian

last: Henderson

first: Steven

last: Wilson

first: Shelly

last: Glase

first: Katherine

last: Munson

first: Guadalupe

last: Hiles

first: Angelica

last: Cates

first: Amir

last: Emamdjomeh

first: Andrew

last: Chu

first: Joseph

last: Farber

first: Jeff

middle: W

last: Kamph

first: Monica

last: Liebert

first: Michelle

middle: T

last: Paulsen

first: Kenneth

last: VanGolen

first: Mats

last: Ljungman

first: Armand

last: Bankhead

first: Phillip

last: Palmbos

first: Kathleen

last: Day

first: Mark


title: Construction of Vascularized Adipose Organoids and Their Application in Drug Efficacy Evaluation.

city: beijing

first: Sen

last: Li

state: beijing

address: No. 2 Yabao Road, Chaoyang District

institute: Capital Institute of Pediatrics

summary: This study successfully established a three-dimensional (3D) vascularized adipose organoid model using peripheral blood mesenchymal stem cells (PBMSC) to mimic the physiological structure and function of human adipose tissue. Transcriptomic analysis revealed unique gene expression profiles related to adipocyte differentiation, tissue maturation, and metabolic pathways. Additionally, drug intervention experiments demonstrated that Celastrol effectively inhibited both angiogenesis and adipogenesis, while modulating the expression of genes associated with lipid metabolism. The vascularized adipose organoid model developed in this study provides a powerful tool for investigating adipose tissue biology, metabolic disease mechanisms, and drug screening, with promising applications in personalized medicine and regenerative medicine.

overall_design: First, a comprehensive transcriptomic analysis was performed to compare the gene expression profiles of vascularized adipose organoids and standard adipose organoids. Then, vascularized adipose organoids were used to assess the effects of Celastrol, followed by a transcriptomic analysis to compare the gene expression profiles with Celastrol treatment.

first: Fangming

last: Kan

first: Shuhui

last: Ji

first: Haiyang

last: Liu

first: Jianxin

last: Wu


title: RUNX2 regulates aberrant collagen gene expression in keloid fibroblasts

city: Dallas

first: Donald

last: Glass

state: TX

address: 5323 Harry Hines Blvd, Mail Code 9069

department: Dermatology

institute: UT Southwestern Medical Center

summary: Keloids comprise an inflammatory fibroproliferative skin disorder characterized by excessive scarring. Fibroblasts play a pivotal role in skin fibrosis, exhibiting heightened collagen deposition. To investigate the molecular drivers of excessive collagen deposition in keloid, we compared the transcriptome of keloids and adjacent normal skin which demonstrated significant shifts towards bone and cartilage lineages in keloids, along with RUNX2, a key regulator of osteogenic and chondrogenic differentiation, notably upregulated. We then confirmed elevated levels of RUNX2 protein and phosphorylated RUNX2 in keloid tissue and fibroblasts compared to normal skin and normal dermal fibroblasts. To delve into how RUNX2 overexpression could contribute to keloids pathogenesis, we performed siRNA-mediated knockdown of RUNX2 in keloid fibroblasts followed by mRNA-sequencing. The results revealed significant downregulation of collagen genes COL11A1, COL5A3, COL15A1, and COL6A6, in knock-down vs. control groups along with GO enrichment analysis showing perturbation of genes involved in collagen and ECM organization. Further functional studies utilizing Runx2-knockout mice confirmed downregulation of these collagen genes along with reduced dermis thickness and reduced total dermal collagen in Runx2-knockout vs. Runx2- wild mice. These findings underscore the critical contribution of RUNX2 to collagen remodeling in keloid and provide potential therapeutic target.

overall_design:
RNA-seq profiling of primary keloid fibroblasts and their knockdown derivatives (siRUNX2)
RNA-seq profiling of keloid tissue and normal skin controls

first: Sepideh

last: Hamzehlou

first: Neda

last: Vishlaghi

first: John

middle: M

last: Shelton

first: Benjamin

last: Levi

first: Chao

last: Xing

last: Glass II


title: Genome-wide DNA Methylation Analysis Identifies Kidney Epigenetic Dysregulation in a Cystinosis Mouse Model

city: Rome

first: Giusi

last: Prencipe

address: Viale di San Paolo 15

country: Italy

institute: Bambino Gesù Children's Hospital

type: Methylation profiling by genome tiling array

summary: Nephropathic cystinosis is a rare genetic disorder caused by cystine accumulation in lysosomes, resulting in early renal dysfunction and progressive kidney disease. While altered metabolic pathways, oxidative stress, and inflammation have been implicated in disease pathogenesis, the precise mechanisms driving its progression are still not fully understood. Recent studies indicate that epigenetic modifications, particularly DNA methylation (DNAm), play a crucial role in the development of chronic kidney disease. Building on this, we hypothesize that epigenetic dysregulation may also contribute to the progression of cystinosis.Methods. We performed a genome-wide DNAm analysis on the kidneys of 6-month-old Ctns?/? mice, a model for cystinosis, comparing them to wild-type (WT) controls. Our analysis revealed extensive DNAm alterations in cystinotic kidneys, with a marked hypermethylation pattern. These methylation changes were primarily found in genes and pathways crucial for kidney function, particularly those related to the physiology of the proximal tubules. Importantly, these DNAm alterations correlated with changes in gene expression, as validated by qPCR analyses of key genes in WT and Ctns-/- kidneys. Furthermore, in vitro treatment with the demethylating agent decitabine in human proximal tubular epithelial cells led to the upregulation of critical transporter genes, suggesting a potential therapeutic approach. These findings underscore the role of epigenetic regulation in cystinosis progression and suggest that DNAm could serve as a promising target for novel therapeutic strategies.

overall_design: DNA was extracted and analysed from whole kidneys of 6-months-old wild type or cystinotic mice

first: Rossi

last: Marianna Nicoletta

first: Ciolfi

last: Andrea

first: Pedace

last: Lucia

first: Miele

last: Evelina

first: Prencipe

last: Giusi


title: Extracellular Matrix Regulates PD-1 on Tregs via IL-23 contributing to immune suppression in Breast Cancer

city: Milan

first: Annamaria

last: Piva

address: via Amadeo, 42

institute: Fondazione IRCCS Istituto Nazionale dei Tumori

summary: Background. High-grade breast cancer (HGBC) is an aggressive disease with a poor prognosis, highlighting the urgent need for new treatment strategies. The tumor microenvironment (TME), especially the extracellular matrix (ECM), plays a crucial role in tumor progression, therapy resistance, and immune regulation. An ECM-related gene signature (ECM3) is present in approximately 35% of HGBC patients and is associated with aggressive tumors, epithelial-to-mesenchymal transition (EMT), poor clinical outcomes, and increased infiltration of immunosuppressive myeloid-derived suppressor cells (MDSCs).   Methods. We investigated the impact of the ECM on T-cell regulation in HGBC patients, focusing on the correlation between ECM3+ tumors and regulatory T cells (Tregs). Using mouse models, we explored the role of the matricellular protein SPARC, a key component of the ECM3 signature, in modulating PD-1 expression on Tregs. Mechanistic studies were performed to identify the signaling pathway involving SPARC, IL-23, and the transcription factor SATB1. Additionally, the effect of IL-23 blockade on Treg function was evaluated using monoclonal antibodies.  Results. We found a significant correlation between highly suppressive PD-1-negative Tregs and ECM3+ tumors. In mouse models, SPARC downregulated PD-1 expression on Tregs by promoting IL-23 release, which induced SATB1 expression, a repressor of the pdcd1 gene. The selective expression of the IL-23 receptor on Tregs explained the targeted effect of IL-23. Blocking IL-23 with monoclonal antibodies restored PD-1 expression on Tregs and activated T effector cells.Conclusions. These findings enhance our understanding of the immune-regulatory functions of the ECM and highlight potential therapeutic targets for treating high-grade breast cancers by modulating Treg activity and boosting immune responses.

overall_design: This study includes four replicates per condition.

first: Giovanna

last: Talarico

first: Sabina

last: Sangaletti


title: Loss of PTDSS1 in tumor cells improves immunogenicity and response to anti-PD-1 therapy [scRNAseq]

city: Houston

first: Jielin

last: Liu

address: 7455 Fannin St

department: Genitourinary Medical Oncology

institute: MD Anderson Cancer Center

summary: PTDSS1 (Phosphatidylserine synthase 1) encodes an enzyme that facilitates production of phosphatidylserine (PS), which mediates a global immunosuppressive signal. Here, based on in vivo CRISPR screen, we identified PTDSS1 as a target to improve anti-PD-1 therapy. Depletion of PTDSS1 in tumor cells increased expression of IFNγ-regulated genes, including B2m, Cxcl9, Cxcl10, and Stat1, even in the absence of IFNγ stimulation in vitro. Loss of PTDSS1 in tumor cells also led to increased expression of MHC-I, which was associated with enhanced cytotoxicity of CD8+ T cells and increased frequency of an iNOS+ myeloid subset. A gene signature derived from the iNOS+ myeloid cell subset correlated with clinical benefit in patients treated with anti-PD-1 therapy. Moreover, genetic and pharmacological inhibition of PTDSS1 in different tumor models improved anti-PD-1 therapy. Together, our results provide insights on a new therapeutic strategy for overcoming immunosuppression by inhibiting PTDSS1 and provide rationale for development of a combination immunotherapy strategy comprised of PTDSS1 inhibition plus PD-1 blockade.

overall_design: single cell RNA sequencing of WT or Ptdss1 KD tumors


title: Pathology response in primary human Hepatic Stellate cells determined by donor’s phenotype

city: Leiden

first: Eveline

last: Gart

state: Zuid Holland

address: Sylviusweg 71

department: MHR

country: Netherlands

institute: TNO

summary: Introduction: Liver disease has increased worldwide in both developing and developed world. Preclinical research has intensively delved into pathology mechanisms and target identification using hepatic stellate cells. However, there is a lack of knowledge in interindividual variability, fibrosis progression differences and connection of preclinical fibrosis in vitro models with patient subpopulations. Here, we aimed to investigate individual response of human primary hepatic stellate cells (HSC) from distinct (fibrotic/non-fibrotic) donors. Methods: Human primary HSCs from fibrotic (Fibrosis Fscore 3, 4) and non-fibrotic (Fibrosis Fscore 0) donors were cultured and stimulated with TGFβ1 to investigate disease recapitulation and interindividual variability on relevant fibrotic markers (Collagen, Fibronectin, TIMP1) as well as their biological functionality through NGS data. To assess fibrotic phenotype, fibrotic parameters were assayed in the cell/matrix fraction or in conditioned culture media. RNA was isolated and sequenced through next generation sequencing (NGS) to elucidate biological functionality and identify differentially expressed genes (DEGs) using Deseq2 and Ingenuity Pathway Analysis (IPA), respectively. Results: First, all primary HSCs donors (except one) showed induction after fibrosis stimulation with TGFβ1 (4 ng/ml) on the various fibrosis markers (total collagen, TIMP-1 and fibronectin). Of note, on the group level, fibrotic donors showed higher disease memory compared to non-fibrotic evidenced by less DEGs (4919 vs 7631) in the stimulated condition (TGFβ1). In addition, when each donor individually (control and stimulated, separately) was compared against healthy pooled controls (D#5-D#8), three out of four fibrotic donors (D#1, D#2, D#4) showed high upregulation in fibrosis pathways in control condition. Conclusion: Here we show that HSCs cultured in vitro from distinct human donors seem to respond equally to fibrosis induction. However, it is relevant to consider that the in vivo metabolic phenotype is retained in unstimulated conditions, thereby showing metabolic memory when cultured in vitro.

overall_design: Human primary HSCs (Hepatic Stellate Cells) isolated from the livers of fibrotic donors (D1, D2, D3, D4; with Fibrosis scores 3-4 and NAS scores 2-6) and healthy non-fibrotic donors (D5, D6, D7, D8; with Fibrosis score = 0 and NAS scores 1-2) were cultured for 4 days -/+ stimulation with compound combinations (3 treatment types per donor): Control without additions (C), 4 ng/ml TGFβ1 (T), 4 ng/ml TGFβ1 + 5 μM Alk5 (TA). TGFβ1 = Transforming growth factor beta 1. Alk5 = ALK5 kinase inhibitor (ALK5 = TGFβ type I receptor kinase).

first: Manuel

last: González Hernández

first: Lars

last: Verschuren

first: Martien

last: Caspers

first: Martine

middle: C

last: Morrison

first: Jennifer

last: Venhorst

first: Gerard

last: van Westen

first: Beatrice

last: Coornaert

first: Roeland

last: Hanemaaijer


title: Effect of subchronic (3 and 7 weeks) ototoxic (3,3'-iminodipropionitrile, IDPN) exposure on the vestibular epithelium of the rat

first: Jordi

last: Llorens

summary: Several compounds cause auditory and vestibular toxicity by targeting the sensory transducing cells of the inner ear, the hair cells (HC). These compounds, known as ototoxic compounds, may cause vestibular HC apoptosis following high dose acute exposure. However, chronic exposure to low doses has been observed to cause progressive damage. Thus, chronic ototoxic stress first cause detachment and uncoupling of the HC and their post-synaptic neurons, followed by changes in cell shape including stereocilia fusion and ending with extrusion of the HCs from the sensory epithelium towards the luminal spaces of the vestibule. The molecular mechanisms driving these phenomena have not been established. We hypothesized that this response of the vestibular epithelium to chronic ototoxic stress must include specific gene expression responses. The present SubSeries is part of a SuperSeries aimed at identifying these expression responses. Two species, two ototoxic compounds and different times were studied as a strategy to identify the most relevant responses. In the present SubSeries, the expression response of the vestibular epithelium is studied in rats exposed to 3,3'-iminodipropionitrile (IDPN) for 3 or 7 weeks.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from vestibular epithelia of control rats and rats after subchronic (3 and 7 weeks) ototoxic (3,3'-iminodipropionitrile, IDPN) exposure.

first: Marta

last: Gut

first: Anna

last: Esteve-Codina

first: Beatriz

last: Martín-Mur

first: Alejandro

last: Barrallo-Gimeno


title: Effect of mitochondria-targeted derivative of curcumin (Mitocurcumin; MC ) on gene expression in human Triple Negative Breast Cancer cell line, MDA-MB-231.

city: Mumbai

first: Shivani

middle: R.

last: Nandha

address: Trombay

country: India

institute: Bhabha Atomic Research Centre

summary: RNA sequencing was performed to elucidate the anti-cancer mechanism of action of mitocurcumin in MDA-MB-231 Triple Negative Breast Cancer cells.  Transcriptomic analysis revealed that mitocurcumin-treatment led to significant down-regulation of genes regulating cell proliferation, differentiation, vasculature development and DNA-binding transcription activator activity while the significantly up-regulated genes associated with starvation, oxidative stress, response to unfolded proteins and topologically incorrect proteins and intrinsic apoptosis. Mechanistically, in vitro and transcriptomics confirmed mitocurcumin-mediated induction of mitochondrial oxidative stress, bioenergetic stress and proteotoxic stress culminating in apoptosis.

overall_design: Gene expression profiling analysis of Human Triple Negative Breast Cancer cell line, MDA-MB-231 cells,  treated with 5µM mitocurcumin for 9h (Treatment group) and DMSO-vehicle treated cells (Control group)

middle: R

first: Rahul

last: Checker


title: RNA Sequencing Identification of MC38-P and Its Liver Metastatic Derivatives, MC38-LM3a and MC38-LM3b [Bulk RNA-seq]

first: Shufang

last: Liang

summary: Mouse-derived MC38 cells were subjected to in vivo selection to obtain colorectal cancer liver metastatic derivatives, MC38-LM3a and MC38-LM3b. Subsequently, their gene expression characteristics were identified through transcriptomic sequencing.

overall_design: RNA-seq was performed on MC38 parental cells, MC38-LM3a, and MC38-LM3b, with each group containing three biological replicates

first: Yinheng

last: Luo


title: Comparative DNA methylation profiling of human and murine ALK-positive B-cell neoplasms

city: Ulm

first: Selina

last: Glaser

address: Albert-Einstein-Allee 11

country: Germany

institute: Ulm University and Ulm University Medical Center

summary: Structural genomic variants leading to anaplastic lymphoma kinase (ALK) gene fusions and aberrant expression of the ALK tyrosine kinase are the hallmark of subtypes of T- and B-lineage neoplasms, namely ALK-positive anaplastic large lymphoma (ALCL) and ALK-positive large B-cell lymphoma (LBCL). The latter is a rare aggressive lymphoma, which has been initially identified as a variant of diffuse LBCL (DLBCL) with plasmablastic features. Here, we performed comparative DNA methylation profiling of human and murine ALK-positive B-cell neoplasms. Array-based DNA methylation data from ALK-positive LBCL samples of eight patients were compared to that of DLBCL (n=75), multiple myeloma (MM, n=24), ALK-positive ALCL (n=12) and normal B-cell populations (n=93). ALK-positive LBCLs share a distinct DNA methylation signature similar to that of MM, characterized by lower global DNA methylation levels compared to DLBCLs and normal B-cell populations. DNA methylation alterations in ALK-positive LBCL were predominantly located in heterochromatic and polycomb-repressed regions. The epigenetic age and relative proliferative history of ALK-positive LBCL were intermediate between MM and DLBCL. B-cell neoplasms in NPM::ALK transgenic mice showed a similar hypomethylated signature when compared to normal murine B cells. Cross-species comparison indicated conservation of chromatin states and pathways affected by hypomethylation. Together, the findings suggest that in line with their phenotypical appearance human and murine ALK-positive B-cell lymphomas share an epigenetic profile more closely resembling that of plasma cell neoplasias than that of DLBCLs.

overall_design: Six samples from plasmacytomes derived from NPM::ALK transgenic mice were collected and profiled in duplicates. In addition, three samples from normal B cells with a germinal center phenotype (CD19+, B220+, CD38 low, FAS high and YFP+ ) were investigated. The samples were analyzed using the Infinium MouseMethylation BeadChip array.

first: Reiner

last: Siebert


title: Comparative DNA methylation profiling of human and murine ALK-positive B-cell neoplasms [EPIC]

overall_design: We collected 1 sample from patient with ALK-positive large B-cell lymphoma after treatment with Crizotinib. From the same patient a patient-derived xenograft model was generated. In addition, 7 ALK-positive anaplastic large lymphoma were profiled. The samples were analyzed using the MethylationEPIC BeadChip array.


title: Iron reshapes polyamine metabolism through controlling exosomal miR-33a secretion to remodel extracellular matrix in tumor microenvironment

city: wuhan

first: Wei

last: Yan

state: Hubei

address: Bayi Street 229 in Wuchang district

department: College of life science

institute: Wuhan University

summary: Tumor progression depends on the bidirectional interactions between cancer and stroma in the heterogenous tumor microenvironment (TME) partially through extracellular vesicles (EVs). However, the secretion mechanism and biological effect of cancer cell-derived EVs on tumor survival under starvation is poorly defined. Here, we demonstrate cancer cells selectively secrete miR-33a with the assistance of protein ACO1 under glucose starvation and lower iron level, which affiliates the binding capability of miR-33a and ACO1. Exosomal miR-33 suppresses putrescine biosynthesis by targeting AGMAT in tumor stroma, where putrescine inhibits the  expression of demethylase KDM5C. TIA1 gene, stress granule (SG) marker, is tightly regulated by miR-33a/KDM5C axis. Exosomal miR-33a diminishes the formation of SGs in tumor stroma but inducing more fibronectin secretion into TME. Collectively, our study reveals tumor secrets distinct EV cargoes to remodel the SGs and extracellular matrix of TME to gain survival possibility, highlighting a novel regulatory mechanism of iron and nutrient level on EV secretion in TME.

overall_design: Chromatin immunoprecipitation DNA-sequencing(ChlP-seq) for the histone  modification H3K4me3 in mouse primary CAF cells.

first: Sheng

last: Hu

first: Xu

last: Li


title: Comparative DNA methylation profiling of human and murine ALK-positive B-cell neoplasms [450K]

overall_design: We collected 6 samples from patients with ALK-positive large B-cell lymphoma and 1 from the LM1 cell line. The samples were analyzed using the Infinium HumanMethylation450 BeadChip array.


title: LIGHT induces psoriais and atopic dermatitis related genes in keratinocyte

city: La Jolla

first: Michael

last: Croft

state: CA

address: 9420 Athena Circle

institute: La Jolla Institute for Immunology

summary: LIGHT upregulated a varity of genes in the human keratinocytes that are found to be highly expressed in the patients with psoriais and atiopic dermatitis. RNA was isolated from 3 different replicates per group, using a Qiagen kit and subjected to RNA-seq analysis.

overall_design: Human epidermal keratinocytes from neonates were purchased from ATCC (NHEK, PS-200-010, ATCC, Manassas, VA) and grown in Dermal Cell Basal Medium (PCS-200-030, ATCC). 3x105 cells/well were cultured in triplicates using a 6-well format plate and stimulated with predetermined optimal concentrations of human rLIGHT (100 ng/ml) for 48 hrs. Controls received PBS.

first: Rinkesh

last: Gupta

first: Kai

last: Fung


title: Decoding Trp53 regulatory program with knockout cell transcriptomic landscape analyses [stRNA-seq]

city: Hanzhou

first: Guoji

last: Guo

address: Yuhangtang street 866

department: Zhejiang University School of Medicine

institute: Center for Stem Cell and Regenerative Medicine

summary: For decades, researchers have devoted great efforts to studying the tumor suppressor gene Trp53, however, our understanding of Trp53 regulation has never reached either organism-scale or single-cell resolution. Here, we performed spatial RNA analysis to confirm the Trp53 KO-induced tumor initiation states.

overall_design: Tissues of Trp53-/- and Trp53+/+ mice at different ages were isolated and embedded in Optimal Cutting Temperature compound (OCT, Sakura Tissue-TEK) on dry ice, followed by cryosectioning, fixation, tissue transferring to slides, spatial cDNA library construction, high-throughput sequencing, and bioinformatics analysis.

first: Xiaoping

last: Han

first: Xinru

last: Wang

first: Yuqing

last: Mei

first: Xueyi

first: Jingjing

first: Peijing

last: Zhang

first: Hanyu

last: Wu


title: Candida albicans and Staphylococcus aureus reciprocally promote their virulence factor secretion and pro-inflammatory effects

city: Amsterdam

last: van Leeuwen

address: Science Park 904

department: MAD

institute: University of Amsterdam

summary: Co-infections of Candida albicans and Staphylococcus aureus can significantly increase morbidity and mortality. This synergism is linked to the interactions between C. albicans and S. aureus that allow for staphylococcal co-invasion and dissemination. While it is known that virulence factors contribute to this process, the effect of C. albicans-S. aureus coculturing on virulence factors composition and macrophage-mediated inflammation remain unknown. In this study, we used mass spectrometry-proteomics to investigate the effect of coculturing on the composition of the >3 kDa protein fraction of the S. aureus and C. albicans secretome, as well as the secretomal cytotoxicity and proinflammatory effects on human oral cells and immune cells. Results showed that coculturing of C. albicans and S. aureus promoted the secretion of 7 cytolytic, 11 proteolytic, and 3 lipolytic extracellular virulence factors (ECVFs). While the majority of differentially released C. albicans ECVFs were attributable to Als1/Als3-mediated interactions, changes in S. aureus secretomal ECVF composition were mainly attributable to the presence of C. albicans or its pH maintenance. By analysing both secreted and non-secreted virulence factors, it appears that coculturing promotes C. albicans hypha formation together with β-glucan masking, suggesting that coculturing enhances both C. albicans invasion and immune evasion. In addition, coculturing increased the cytotoxic potential of the secretome towards human oral epithelial cells and macrophages compared to the summed cytotoxic effect of both monoculture secretomes. Under non-cytotoxic conditions, the secretome of C. albicans-S. aureus coculture promoted macrophage activation and increased gene transcription of pro-inflammatory pathways compared to monoculture secretomes. Surprisingly, ALS1/ALS3 knock out has marginal effects on the secretome-increased proinflammation in macrophages. Our findings support that C. albicans and S. aureus reciprocally promotes their virulence potential, cytotoxicity, and proinflammatory effects, which may provide insights into the synergistic lethality during their coinfection in vivo.

overall_design: RNA-seq profiling of THP-1-derived macrophages to investigate the transcriptional response to medium with the secretome of Staphylococcus aureus ATCC12600 and/or Candida albicans SC5314 wildtype or ALS1/ALS3 knock out.

first: Raymond

last: Pasman

first: Bastiaan

last: Krom

first: Martijs

last: Jonker

first: Wim

last: de Leeuw

first: Gertjan

last: Kramer

first: Stanley

last: Brul

first: Sebastian

last: Zaat

first: Jianbo


title: Androgen deprivation-mediated activation of AKT is enhanced in prostate cancer with TMPRSS2:ERG fusion [microarray]

city: Boston

first: Steven

last: Balk

address: 3 Blackfan circle

institute: BIDMC

summary: The TMPRSS2:ERG gene fusion (T:E fusion) in prostate adenocarcinoma (PCa) puts ERG under the androgen receptor (AR) regulated expression of TMPRSS2. The T:E fusion is frequently associated with PTEN loss, and is highly correlated with decreased expression of INPP4B, both of which may compensate for ERG-mediated suppression of PI3K/AKT signaling. We confirmed in PCa cells and a mouse PCa model that ERG suppresses AKT activation, and that one potential mechanism is through downregulation of IRS2. In contrast, ERG knockdown did not increase INPP4B, suggesting its decreased expression is indirect and reflects selective pressure to suppress INPP4B function. Notably, INPP4B expression is similarly decreased in PTEN-intact and PTEN-deficient T:E fusion tumors, suggesting selection for a function distinct from regulation of PI3K activity. As ERG expression in T:E fusion tumors is AR regulated, we further assessed the extent to which AR inhibition increased AKT activity in T:E fusion tumors. T:E fusion positive versus negative PDXs had greater increases in AKT activity after castration. Moreover, in a neoadjuvant trial of AR inhibition prior to radical prostatectomy we similarly found greater increases in AKT activation in the T:E fusion tumors. Together these findings indicate that AKT activation may mitigate the efficacy of AR targeted therapy in T:E fusion PCa, and that these patients may most benefit from combination therapy targeting AR and AKT.

overall_design: 6 samples

first: Fen

last: Ma

first: Sen

last: Chen

first: Carla

last: Calagua

first: Seiji

last: Arai

first: Fang

last: Xie

first: Olga

last: Voznesensky

first: Larysa

last: Poluben

first: Eva

last: Corey

first: Changmeng

last: Cai

first: Yuzhuo

first: David

last: Einstein

first: Mary-Ellen

last: Taplin

first: Huihui

last: Ye

first: Adam

middle: G

last: Sowalsky

first: Joshua

last: Russo

first: Xin

last: Yua


title: Human iPSC-Derived Mononuclear Phagocytes Improve Cognition and Neural Health across Multiple Mouse Models of Aging and Alzheimer's Disease

city: Los Angeles

first: Shaughn

last: Bell

address: 8700 Beverly Blvd

department: Regenerative Medicine Institute

institute: Cedars-Sinai Medical Center

summary: Young blood or plasma and young bone marrow improves cognitive function in aged animals, though the cell type responsible for these regenerative effects remains unknown. The current study used induced pluripotent stem cells (iPSCs) to assess the potential of mononuclear phagocytes as a therapeutic for age-associated cognitive decline, as iPSCs provide a source of autologous blood cells without the risk of immune rejection or graft vs. host disease. Human iPSCs differentiated into mononuclear phagocytes (iMPs) were administered to aging, genetically immunocompromised NOD scid gamma mice via tail vein injection. Aging mice receiving iMP treatment showed significant improvements in behavioral tasks relying on spatial working memory and on hippocampus-dependent short-term memory. iMP treatment also had significant effects on several key neural health markers. Expression of the synaptic transporter, VGLUT1, was decreased in untreated aging mice, and levels were restored in aging mice treated with iMPs. Aging mice also had increased numbers of astrocytes and microglia, as well as decreased microglial branching, which were all reversed by iMP treatment. Profiling of the plasma via proteomics and the hippocampus via single nuclei RNA sequencing identified several pathways that may mediate the effects of iMPs. snRNA-seq analysis also revealed that iMP treatment increased a subpopulation of hippocampal mossy cells in aging mice. iPSCs offer an autologous therapy and based on a range of benefits, iPSC-derived mononuclear phagocytes are a promising new therapeutic strategy for age-associated declines in cognition and neural health.

overall_design: Single nucleus sequencing of hippocampus region of mice:  1) Mouse hippocampus from young animals treated with vehicle (2 animals); 2) Mouse hippocampus from aging animals treated with vehicle (3 animals); 3) Mouse hippocampus from aging animals treated with iMPs (3 animals)

first: V

last: Moser

first: Luz

middle: J

last: Dimas-Harms

first: Rachel

last: Lipman

first: Jake

last: Inzalaco

first: Michelle

last: Alcantara

first: Erikha

last: Valenzuela

first: George

last: Lawless

first: Simion

last: Kreimer

first: Sarah

last: Parker

first: Helen

middle: S

last: Goodridge

first: Clive

middle: N

last: Svendsen