title: Inhibition of autophagy and Hsp90 activity alleviate metabolic and infectious diseases by regulating hepatic lipid deposition and ROS accumulation in zebrafish larvae with hepatobiliary syndrome and/or GCRV-II infection

city: Wuhan

first: siyao

last: Zheng

address: No.7, Donghu South Road, Wuchang

institute: Institute of Hydrobiology, Chinese Academy of Sciences

summary: Hepatobiliary syndrome is caused by the impairment of liver fat metabolism in fish, which leads to the weakening or loss of hepatobiliary function. Also, metabolic hepatobiliary syndrome leads to low immune resistance of diseased fish, which is easily induce fish to be infected with other bacterial or viral diseases. By treating wild-type zebrafish larvae with different concentrations of dexamethasone, we found that dexamethasone induced hepatomegaly, hepatic lipid deposition and reduced survival in zebrafish. In addition, dexamethasone treatment combined with GCRV-II infection aggravated lipid deposition in the liver and impaired the survival of zebrafish larvae. Transcriptome data showed that autophagy signaling pathways and blood pressure regulation pathways are significantly enriched. Furthermore, we treated zebrafish larvae with autophagy inhibitor and HSP90 inhibitor, dexamethasone and GCRV-II infection, then found that the survival of zebrafish larvae was improved, liver lipid deposition was attenuated, and ROS production was greatly reduced. In conclusion, this study provides insights into the regulation of immune metabolism in zebrafish hepatobiliary syndrome and GCRV-II infection, and provides potential molecular targets for the prevention and control of metabolic disease-induced infectious diseases in other cyprinids.

overall_design: To clarify lipid accumulation in the liver of zebrafish, oil red O staining was used to stain zebrafish larvae and photographs were taken under a stereomicroscope. The ROS production of zebrafish larvae was investigated by oxidation-sensitive fluorescent probes, and pictures were taken under a stereoscopic fluorescence microscope. Moreover, key genes in significantly affected signaling pathways were analyzed by transcriptomic analysis.

first: Mingxian

last: Chang

first: Siyao


title: An emergent disease-associated motor neuron state precedes cell death in a mouse model of ALS [scRNA-Seq]

status: Public on Aug 27 2025

city: Stanford

first: Olivia

last: Gautier

state: CA

address: 279 Campus Dr

country: USA

institute: Stanford University

type: Expression profiling by high throughput sequencing

summary: To uncover molecular determinants of motor neuron degeneration and selective vulnerability in amyotrophic lateral sclerosis (ALS), we performed longitudinal single-nucleus RNA sequencing, paired single-nucleus RNA and ATAC sequencing, and MERFISH spatial transcriptomics from control and SOD1-G93A mouse spinal cords. For the final snRNA-seq analysis, control experiments from Blum et al., Nat Neurosci, 2021 (GEO accession: GSE161621) were also used.

overall_design: Nuclei were isolated from the spinal cords of control and SOD1-G93A mice at early-stage (~P65), mid-stage (~P100), and end-stage (~P125). All mice carried ChAT-IRES-Cre and ROSAnT-nG alleles, which labeled nuclei from cholinergic neurons with GFP and nuclei from other cell types with tdTomato. Fluorescence-Activated Nuclei Sorting (FANS) was performed to enrich GFP+ cholinergic nuclei while also collecting tdTomato+ non-cholinergic nuclei. Following nuclei sorting, either snRNA-seq (Chromium Single Cell 3′ Reagent Kit v3, 10x Genomics) or multiome ATAC + gene expression profiling (Chromium Single Cell Multiome ATAC + Gene Expression v1, 10x Genomics) was performed according to manufacturer protocols, and libraries were sequenced on an Illumina NextSeq 550 or NovaSeq 6000.

first: Jacob

middle: A

last: Blum

first: Thao

middle: P

last: Nguyen

first: Sandy

last: Klemm

first: Mai

last: Yamakawa

first: Nasa

last: Sinnott-Armstrong

first: Yi

last: Zeng

first: Chung-ha

middle: O

last: Davis

first: Juliane

last: Bombosch

first: Lisa

last: Nakayama

first: Kevin

last: Guttenplan

first: Derek

last: Chen

first: Arwa

last: Kathira

first: Luke

last: Zhao

first: Jessica

middle: E

last: Rexach

first: William

middle: J

last: Greenleaf

first: Aaron

middle: D

last: Gitler


title: An emergent disease-associated motor neuron state precedes cell death in a mouse model of ALS [multiome]

first: Olivia

last: Gautier

type: Genome binding/occupancy profiling by high throughput sequencing


title: Transcriptomics profiling of singleton and twin placentas in the absence or presence of preeclampsia.

status: Public on Aug 28 2025

city: Chicago

last: Ackerman

state: Illinois

address: 820 South Wood Street, MC 808, Dept. of Obstetrics & Gynecology

department: Obstetrics and Gynecology

institute: University of Illinois Chicago College of Medicine

summary: Twin pregnancies incur a higher risk for preeclampsia (PE) than singletons, but the pathogenesis might differ. To better understand this, we performed RNA sequencing on 32 individual dichorionic (D) and monochorionic (M) twin placental samples grouped by clinical PE diagnosis and 10 newly sequenced singleton (S) PE placentas.

overall_design: We performed RNA sequencing (RNA-seq) using 42 human placental villous tissue samples grouped as follows: (1) singleton (S) PE placental samples with a range of clinical PE disease severities (n=10); and (2) 32 individual villous placenta samples from 16 diamniotic twin pregnancies classified by chorionicity (dichorionic, D; and monochorionic, M) and PE diagnosis: No PE D (n=7 pregnancies), No PE M (n=2 pregnancies), PE D (n=5 pregnancies), and PE M (n=2 pregnancies). In addition, 3 new samples from placentas used in our prior study (corresponding to S06 [GSM6175121], S18 [GSM6175133], and S20 [GSM6175135] from GSE203507) were extracted and prepared using the paired-end library and sequencing protocol to assess how this compared to the original sequencing protocol (single-end, 50 bp reads).

first: Irina

last: Buhimschi

first: Catalin

middle: S


title: Bulk RNA sequencing of liver biopsy-derived organoids from patients with alcohol-associated liver disease and paired tissues

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

country: Spain

institute: CIBEREHD

summary: RNA sequencing was performed on liver organoids obtained from biopsies (b-Orgs) and paired tissues collected at different stages of alcohol-associated liver disease (ALD) using biliary (BEC) and hepatocyte (HEP) culture conditions. Different "generations" and passages of b-Orgs cultured with HEP medium were also sequenced. Besides, sequencing was also performed on vehicle and b-Orgs treated with Alcohol-associated hepatitis (AH)-medium. Finally, standard cholangiocyte organoids (Chol-Orgs) generated by dissociation of end-stage liver resections from ALD patients were sequenced.

overall_design: b-Orgs generated using BEC (n=6) and HEP (n=30) culture conditions from patients with ALD were compared to standard Chol-Orgs obtained by dissociation of ALD end-stage liver resections (n=3). Transcritomic stability on b-Orgs generated with HEP medium was assessed by comparing consecutive b-Org "generations" (T0, n=3; T0B, n=3; T0C, n=3) and passages (P1, n=3; P3, n=3). Moreover, b-Org resemblance to their parental tissue was investigated by comparing whole liver biopsy tissue from patients at advanced (n=3) and early (n=3) stages to paired b-Orgs generated with HEP medium. Finally, vehicle (n=4) and b-Orgs treated with AH-medium (n=4) were compared to assess how b-Orgs could model ALD progression.

first: S

last: Ariño

first: P

last: Sancho-Bru


title: The multiscale distribution of radiation-induced DNA damage and its impact on local genome structure

city: Knoxville

first: Rachel

middle: Patton

last: McCord

state: TN

address: 309 Mossman Bldg. 1311 Cumberland Ave

department: BCMB

institute: University of Tennessee

summary: The three-dimensional genome structure is critical for the regulation of gene expression and repair of DNA damage. While previous work has characterized genome-wide sites of DNA damage caused by etoposide or nucleases, the distribution of double-strand breaks (DSBs) caused by external radiation and how these interact with the 3D genome organization is less well understood. Here, we measure the genomic landscape of radiation-induced DNA damage using END-seq in fibroblasts and lymphoblasts after exposure to 5 Gy X-rays. We identify frequently broken regions and investigate the 3D genome properties around these breaks with Hi-C data. We observe that the distribution of robust breaks correlates with transcriptional and chromatin features of the genome. Transcriptionally active and decondensed regions, such as chromosome 19, the A compartment, and topologically associating domain (TAD) boundaries, show pronounced break probability. We also find evidence of DSB-induced loop formation in the vicinity of frequent radiation-induced breaks. Our data reveal that pre-existing 3D genome architecture influences the distribution of radiation-induced DSBs and that these breaks reshape local chromatin landscapes, advancing our understanding of genome instability.

overall_design: BJ-5ta adhesion cells were cultured and passaged at a density of 80%. GM12878 suspension cells were cultured and passaged at around 500,000 cells per 1 mL of medium. For irradiation experiments, BJ-5ta cells were grown to confluency, and GM12878 cells were grown to a density of 1  106 cells per 1 mL medium prior to 5 Gy X-ray exposure. END-seq experiments were performed in BJ-5ta, GM12878 on control and X-ray treated conditions. U2OS-ER-AsiSI and BJ-5ta-ER-AsiSI cells were cultured with puromycin selection. For DNA damage induction, both cells were seeded without puromycin treatment and treated with 300 nM 4-hydroxytamoxifen (4OHT) for 4 h and 6 h, respectively. END-seq experiments were performed in U2OS-ER-AsiSI and BJ-5ta-ER-AsiSI cells on untreated and treated 4OHT conditions.

first: Heng

last: Li

first: Tianchun

last: Xue


title: RNA-seq Analysis of Drosophila melanogaster Heads Harvested 4-Hours Post-PenetratingTraumatic Brain Injury

city: Madison

first: Grace

last: Boekhoff-Falk

state: WI

address: 1111 Highland Ave.

department: Cell and Regenerative Biology

institute: UW-Madison

summary: We are utilizing an adult penetrating traumatic brain injury (PTBI) model in Drosophila to investigate early regenerative mechanisms after damage to the central brain. Here we incorporate RNA-seq analyses to identify candidate pathways that may trigger cell proliferation following PTBI. We find that transcript levels for components of both Toll and Immune Deficiency (Imd) innate immunity pathways are rapidly and highly upregulated post-PTBI. We then tested mutants for the NF-κB transcription factors of the Toll and Imd pathways, Dorsal-related immunity factor (Dif) and Relish (Rel) respectively. Induction of transcripts for antimicrobial peptide (AMP) levels are substantially elevated after PTBI, however their levels revert to near baseline within 24 hours. These results indicate that the innate immunity pathways play an integral role in the regenerative response. Innate immunity previously has been implicated as both a potentiator and an inhibitor of regeneration. Our work suggests that modulation of innate immunity may be essential to prevent adverse outcomes.

overall_design: RNA-Seq analysis from isolated from heads of young male Drosophila melanogaster collected within 6 hrs of eclosion generated by our 'standard cross' =  w; UAS-mCD8-GFP;; OK107-GAL4 X yw  at four hours after PTBI to both hemispheres of the central brain and from the heads of age- and sex-matched controls without injury. Samples are divided into 3 biological replicas, each from ~100-120 heads.  w; UAS-mCD8-GFP;; OK107-GAL4 X yw  at four hours after PTBI to both hemispheres of the central brain and from the heads of age- and sex-matched controls without injury. Samples are divided into 3 biological replicas, each from ~100-120 heads.

first: Khailee

last: Marischuk

first: Shawn

last: Ahern-Djamali

first: Kassi

middle: L

last: Crocker


title: Preadipocyte uncoupling protein 1 expression invoked by fibroblast growth factors imprints on post-differentiation white and brown adipocyte function [iBAT]

city: Freising

first: Katharina

last: Küllmer

state: Bavaria

address: Gregor-Mendel Straße 2

country: Germany

institute: Technical University of Munich

summary: The presence of uncoupling protein 1 (UCP1) is a hallmark of thermogenic adipocytes and enables heat production by dissipating energy from mitochondrial proton motive force as heat. The purpose of its recently discovered presence in preadipocytes in response to certain fibroblast growth factors (FGFs) remains elusive. In this study, we systematically investigated the potential of all paracrine FGFs to invoke Ucp1 expression in murine preadipocytes derived from interscapular brown and inguinal white adipose tissue. The factors FGF2, FGF4, FGF8, and FGF9 induced Ucp1 expression in undifferentiated preadipocytes, with FGF2 acting most potently and rapidly. This premature Ucp1 induction did not translate into increased Ucp1 thermogenic activity after full adipogenic differentiation. Notably, preadipocyte treatment with FGFs and parallel Ucp1 expression led to a sustained suppression of interferon-stimulated genes after differentiation. Preadipocyte Ucp1 was required and sufficient for this lasting imprint. Thus, FGF-induced Ucp1 expression in preadipocytes programs a lasting post-differentiation anti-inflammatory status.

overall_design: Immortalized brown preadipocytes (Gantert et al., 2021) were cultured in DMEM supplemented with 10% FBS and treated with 5.5 nM FGF8 or vehicle control at ~80% confluency for 48 h. Following pretreatment, cells were either harvested directly or subjected to adipogenic differentiation using the established protocol described in Gantert et al. (2021) (2 days induction followed by 7 days differentiation). Samples were collected after pretreatment, or on day 3 or day 7 of differentiation. Total RNA was isolated using the Promega kit. Library preparation was performed usigng the Illumina kit, and sequencing was carried out at Novogene.

last: Kuellmer

first: Tobias

last: Fromme


title: Distinct 5′ and 3′ Coverage Biases Shape Transcriptome Interpretation in Nanopore Direct RNA versus PCR-cDNA Sequencing

city: Oxford

first: Adam

last: Cribbs

address: Windmill Road

department: NDORMS

country: United Kingdom

institute: University of Oxford

summary: Long-read RNA sequencing enables isoform-resolved transcriptomics, but library preparation introduces systematic biases that shape biological interpretation. We benchmarked Oxford Nanopore’s two protocols—PCR-cDNA and direct RNA—using SKMM2 myeloma cells stimulated with interleukin-6 (IL-6) and ERCC synthetic spike-ins. Direct RNA produced longer, higher-quality reads and more high-confidence isoforms, but showed pronounced 5′ coverage loss. PCR-cDNA yielded shorter fragments with 3′ underrepresentation, detecting more low-abundance transcripts at reduced confidence. Protocol-specific biases had major consequences: differential expression analysis revealed limited overlap in IL-6–responsive genes, and pathway enrichment was broader in direct RNA. At the isoform level, differential transcript usage was almost entirely protocol-specific, with case studies (e.g. RPL22L1, GRB2, RNF220) illustrating concordance and divergence. ERCC controls confirmed these biases as technical rather than biological. Together, our results show that while both methods provide accurate gene-level quantification, transcript-level conclusions depend critically on protocol choice, highlighting the need for careful selection in long-read transcriptomics.

overall_design: SKMM2 multiple myeloma cells were cultured and treated in biological triplicates with either interleukin-6 (IL-6, 1 ng/mL, 18 h) or vehicle control (0.2% BSA). Total RNA was extracted and used to prepare sequencing libraries with two Oxford Nanopore Technologies (ONT) protocols: (i) PCR-cDNA sequencing (SQK-PCB111.24, 14 PCR cycles for SKMM2 RNA, 16 cycles for ERCC spike-ins) and (ii) direct RNA sequencing (SQK-RNA004). Each protocol was applied to both IL-6–treated and control samples, enabling direct benchmarking of protocol-specific biases. ERCC synthetic RNA spike-ins were sequenced in parallel as external controls. Libraries were sequenced on ONT PromethION flow cells (R9.4.1 for PCR-cDNA, RNA flow cells for direct RNA) with live base-calling. Downstream analyses included gene- and isoform-level quantification, differential expression, pathway enrichment, and differential transcript usage.

first: Cribbs

last: Adam


title: AoSho1 and AoOpy2 are involved in the regulation of mycelial growth, sporulation, osmoregulation, and pathogenicity in Arthrobotrys oligospora

city: a

first: Li

last: Xiaoli

address: a

country: China

institute: YNU University

summary: Arthrobotrys oligospora, a widely distributed nematode-trapping fungus, utilises adhesive mycelial nets (traps) to capture nematodes. As key components of the MAPK cascade, Sho1 and Opy2 are critical in the fungal stress response. This study examined the roles of homologous Sho1 (AoSho1) and Opy2 (AoOpy2) through gene knockdown, phenotypic analysis, and multi-omics approaches. The results revealed that knockdown of Aosho1 and Aoopy2 led to reduced mycelial growth, a significant decrease in spore production, trap formation, and nematode predation capacity. Furthermore, deletion of Aosho1 and Aoopy2 increased autophagic activity and heightened sensitivity to osmotic stress. Transcriptome analysis indicated that AoOpy2 functions as a multifaceted regulator in fungal growth, development, and environmental adaptation. Metabolomics data also suggested that AoSho1 and AoOpy2 are involved in several metabolic pathways. In conclusion, AoSho1 and AoOpy2 are essential for mycelial growth, osmoregulation, and the pathogenicity of A. oligospora. This study lays the groundwork for understanding the roles and potential mechanisms of the MAPK signalling pathway in the development and pathogenicity of nematode-trapping fungi.

overall_design: RNA_seq profiling of wildtype Arthrobotrys oligospora ATCC24927 and knockdown mutants Aoopy2 at 0 h and 18 h of nematode induction.

first: Xiaoli

first: Jinkui

last: Yang

first: Lirong

last: Zhu


title: Unraveling the role of CACNA1F, RASAL1, GARIN4, and TRIM56 in common opioid side effects via transcriptomic analysis of differentiated neuron-like SH-SY5Y cells

city: Freiburg im Breisgau

first: Aly

last: Abotaleb

institute: Medical Center – University of Freiburg

summary: Opioids remain indispensable for pain management but their use is limited by significant side effects, including respiratory depression, constipation, tolerance, addiction, and immunosuppression. Although much is known about their mechanism of action, the effects of acute opioid exposure on transcriptional responses have not yet been fully characterized. We performed a transcriptomic analysis of differentiated neuron-like SH-SY5Y cells exposed to five opioid ligands, namely, morphine, TRV130, metamorphine, β-endorphin, and naloxone. After incubation for 15 minutes, the cells were harvested and processed for RNA sequencing via the Illumina NovaSeq 6000 platform. Differential gene expression analysis was performed with DESeq2, and pathway enrichment was conducted via GO, KEGG and Reactome. Individual comparisons between each opioid-treated group and the control group revealed no statistically significant transcriptional changes. However, when all the agonist-treated samples were pooled and compared with the control samples, we identified several significantly downregulated genes (adjusted p < 0.05). Specifically, we observed alterations in the expression of the genes CACNA1F, RASAL1, GARIN4, and TRIM56, which are involved in calcium signaling, synaptic plasticity, the immune response, and reproductive function. CACNA1F downregulation may affect neuronal excitability and retinal signaling; RASAL1 suppression could impact synaptic maturation and memory; GARIN4 is associated with sperm morphology; and TRIM56 downregulation has an immunomodulatory effect, all of which aligns with known opioid-induced side effects. Our findings demonstrate that even short-term opioid exposure can initiate subtle but functionally relevant transcriptional changes. These early responses highlight the potential of transcriptomic profiling to uncover the molecular mechanisms underlying opioid pharmacodynamics and side effects. This approach offers deeper insights into opioid action and supports the development of safer analgesics with fewer systemic adverse effects.

overall_design: MRNA-seq analysis of differentiated neuron-like SH-SY5Y cells after treatment with opioids

first: Nguyen Phan Khoi

last: Le

first: Sara

last: Tucci

first: Martin J.

last: Hug

first: Evelyn

last: Lamy

first: Stefan

last: Günther


title: Fine Mapping and Functional Characterization of qKRN5.04b Reveals ZmGrx5 as a Domestication-Selected Regulator of Kernel Row Number in Maize

city: Shenyang

first: Wei

last: Xue

state: Liaoning

address: 120 Dongling Rd,Shenhe District

department: College of Agronomy

institute: Shenyang Agricultural University

summary: Kernel row number (KRN) is not only a key agronomic trait influencing maize yield but also a phenotype that underwent significant changes during maize domestication from its wild ancestor, teosinte. Previous studies have identified multiple quantitative trait loci (QTLs) associated with ear morphology on chromosome 5, among which the molecular basis and domestication role of qKRN5.04b remain unclear. To elucidate the function of qKRN5.04b, we constructed a segregating population through hybridization based on recombinant inbred lines derived from near-isogenic lines. Using high-throughput genotyping technologies and rigorously excluding interference from teosinte-derived chromosomal segments elsewhere in the genome, we narrowed the qKRN5.04b interval to a 3.8 Mb region. Transcriptomic analysis of immature maize ears revealed that differentially expressed genes were predominantly enriched in cis-regulatory RNA synthesis pathways, while KEGG pathway analysis indicated significant enrichment in auxin signal transduction. Functional validation showed that Mu insertion mutants of ZmGrx5 reduced kernel row number by two, suggesting ZmGrx5 as a candidate gene underlying qKRN5.04b. Population genetic analysis further demonstrated that ZmGrx5 is the most strongly selected member within the CC-type glutaredoxin (ROXY) family. Collectively, this study provides preliminary insights into the molecular basis of qKRN5.04b and offers valuable clues for understanding ROXY gene domestication and advancing molecular breeding strategies in maize.

overall_design: This study explores transcriptomic variation associated with inflorescence development and kernel row number (KRN) in maize using nearly isogenic recombinant inbred lines (NIRILs) derived from a cross between teosinte and maize. Specifically, two NIRILs, A12 and B46, differing in a defined introgressed segment on chromosome 5 from teosinte (Zea mays ssp. parviglumis), were selected for comparative analysis. Immature ears were collected at the V6–V9 leaf stages and manually dissected under a SZN71 Trinocular Macroscopic Co-visual Stereo Microscope (Soptop, Ningbo, China), selecting ear primordia measuring 1.5–2.0 mm staged between the inflorescence meristem (IM) and paired spikelet meristem (SPM). To ensure sample consistency, spikelets from at least 50 independently grown plants at the same developmental stage were pooled per biological replicate. Three biological replicates were collected for each genotype: M1, M2, and M4 from B46; T3, T5, and T6 from A12.The goal of this experiment was to identify genotype-specific transcriptional programs associated with early inflorescence patterning and KRN variation, thereby contributing to the understanding of domestication-related regulatory changes and informing future maize breeding strategies.

first: Min

first: Fanrui

last: Zeng

first: Hu

first: Alessandra

middle: M

last: York

first: Shunyuan

last: Chen

first: Ronghao

last: Guo

first: Qianyi

last: Huang

first: Kanglan

first: Haishan

last: Luo

first: Fenghai

last: Li

first: Wanli

last: Du


title: RNA-seq of RB1-biallelic inactivation mice and HCC cell lines treated with drug

city: Seoul

first: Wonkyung

last: Kim

address: 88, Olympic-ro 43-gil

country: South Korea

institute: Asan medical center

summary: To investigate the effect of RB1 biallelic inactivation on drug response, RNA-seq analysis was conducted on xenograft mouse models and HCC cell lines following drug treatment.

overall_design: RNA-seq was performed on xenograft mouse tumors with RB1 biallelic inactivation and HCC cell lines under drug treatment and control conditions to investigate transcriptomic changes associated with RB1 loss and therapeutic response.

first: Jihyun

last: An

first: Jin-Sung

last: Ju

first: Bora

last: Oh

first: Eun Ju

last: Yang

first: Yue

last: Pu

first: Li-Jie

first: Joong Sup

last: Shim

first: Chang Ohk

last: Sung

first: Ju Hyun


title: BCL11A deficiency protects epidermis from UVB-induced damage through promotion of autophagy

city: Guangzhou

first: xuyi

last: deng

state: Guangdong

address: No. 1838, North Guangzhou Avenue

institute: Southern Medical University

summary: As a major environmental pathogenic factor for various skin diseases, UVB radiation leads to oxidative stress and biomacromolecule damage. Autophagy is a highly conserved catabolic process and serves as one of the main mechanisms to maintain cellular homeostasis. Here, by CRISPR/Cas9-mediated gene deletion, we demonstrate that the essential transcriptional repressor BCL11A is involved in autophagy regulation and participates in the UVB-induced stress response. BCL11A deficiency increases autophagosome formation and enhances the intensity of autophagy flux with or without UVB stress. Mechanistically, ACSS3, rather than autophagy-related genes, is identified as the direct target gene and transcriptionally repressed by BCL11A. Further, BCL11A deficiency reduces DNA damage and ROS to promote survival and inhibit apoptosis under UVB irradiation, which is blocked by pharmacological inhibition of autophagy or BCL11A overexpression. Collectively, BCL11A deficiency promotes autophagy activation to clear ROS and DNA damage, thereby protecting epidermal cells from UVB-induced death.

overall_design: RNA-seq profiling of wildtype HaCaT cells and the BCL11A knockout HaCaT cells.

first: Xuyi

last: Deng

first: Hui

last: Liu

first: Xiaoxu

last: Wang

first: Xinfeng

last: Dong

first: Zhengzheng

last: Fu

first: Xinli

last: Niu

first: Zhi

first: Peiqi

last: Lian

first: Yinyun

first: Zhenhua

last: Ding

first: Yinghui

first: Meijuan

last: Zhou


title: Convergent evolution through independent rearrangements in the primate amylase locus [Rhesus]

city: Buffalo

first: Charikleia

last: Karageorgiou

state: NY

address: 109 Cooke Hall, Mary Talbert Way

department: Department of Biological Sciences

institute: University at Buffalo

summary: Structurally complex regions of the genome are increasingly recognized as engines of evolutionary convergence due to their propensity to generate recurrent gene duplications that give rise to similar gene expression patterns and traits across lineages. However the mutational mechanisms driving these duplications and the regulatory changes enabling novel expression patterns remain poorly understood. The primate amylase locus, marked by independent gene duplications, provides an ideal model to investigate these dynamics. Leveraging high-quality genome assemblies from 53 primates and multi-tissue transcriptomes from Old World monkeys, we reconstructed the evolutionary history of the recurrent gene duplications across the primate phylogeny. Our data suggest that lineage-specific LTR retrotransposon insertions are associated with initial structural instability, while subsequent duplications are primarily driven by non-allelic homologous recombination. Recurrent independent duplications in rhesus macaques, olive baboons, and great apes gave rise to distinct amylase gene copies with convergent expression in the pancreas and salivary glands. We found that these independent gene duplications are accompanied by episodic diversifying selection on lineage-specific copies, likely driving the emergence of functional divergence. Our comparative analyses in primates indicate that the gene ancestral to great ape AMY1 and AMY2A was expressed in both salivary glands and pancreas in the Catarrhini ancestor. The great ape–specific duplication of this ancestral gene likely facilitated subfunctionalization into salivary gland- and pancreas-specific expression, respectively. Comparative analysis of primate amylase promoter regions reveals regulatory rewiring, driven by motif turnover mediated by structural rearrangements, and partially explaining evolutionary shifts in expression. Together, our findings highlight how structural and regulatory modularity in complex genomic regions drives evolutionary innovation and molecular convergence, and we provide a genomic framework for dissecting these processes across diverse lineages.

overall_design: Two-factor, multi-tissue RNA-seq study profiling amylase gene expression across salivary glands and digestive tissues in Old World monkeys. Biopsies of parotid, submandibular, sublingual, pancreas, and liver were collected from five olive baboons (Papio anubis) and six rhesus macaques (Macaca mulatta); one library per tissue per individual (25 baboon + 30 macaque libraries; biological replication per tissue: n=5 and n=6, respectively). The design is within-subject (multiple tissues from the same animal) to enable tissue contrasts while controlling for individual effects; primary comparisons are salivary glands vs pancreas (and pancreas vs liver) within each species. mRNA libraries were prepared by Azenta/GENEWIZ and sequenced on Illumina HiSeq (2×150 bp). External human datasets (salivary glands from Saitou et al. 2020; pancreas/liver from GTEx v8) were processed in parallel for cross-species context but are not part of this submission.

first: Stefan

last: Ruhl

first: Omer

last: Gokcumen


title: Convergent evolution through independent rearrangements in the primate amylase locus [Baboon]


title: Generating Revitalized Stem Cell-Engineered CAR-NKT Cells for the Treatment of Malignant Pleural Mesothelioma

city: Los Angeles

first: Shuo

last: Li

address: 630 Charles E Young Dr S

institute: UCLA

type: Methylation profiling by high throughput sequencing

summary: Malignant pleural mesothelioma (MPM) is a rare but highly aggressive cancer of the pleural lining, characterized by poor prognosis and limited treatment options. While mesothelin (MSLN)-targeted chimeric antigen receptor (CAR)-engineered T (MCAR-T) cell therapy has shown promise in early clinical trials, current autologous approaches are constrained by complex manufacturing processes and delayed treatment timelines, that are particularly challenging for patients with rapidly progressing MPM disease. Here, we report the development of allogeneic IL-15–enhanced, MCAR-engineered invariant natural killer T (Allo15MCAR-NKT) cells, generated via hematopoietic stem and progenitor cell engineering and a clinically guided, feeder-free culture system. This platform enables the scalable production of CAR-NKT cells with high yield, purity, and clinical-grade suitability. Allo15MCAR-NKT cells exhibit potent antitumor activity in vitro and in multiple in vivo models of MPM, mediated through diverse tumor-targeting mechanisms. These cells also demonstrate a revitalized immunophenotypic profile, characterized by low expression of exhaustion markers and immune checkpoints, suggesting sustained functional potential. Importantly, the therapy exhibits a strong safety profile, with minimal signs of graft-versus-host disease (GvHD), cytokine release syndrome (CRS), or off-tumor toxicity. Collectively, this study presents a clinically translatable, off-the-shelf allogeneic CAR-NKT cell therapy with robust antitumor efficacy and a favorable safety profile for the treatment of MPM.

overall_design: 6 samples, including 3 allogeneic HSPC-derived human cells, and 3 PBMC-derived IL-15-enhanced MCAR-engineered NKT (PBMC15MCAR-NKT) cells were included in this study. Genomic DNA was isolated from experimental samples using a QIAGEN DNeasy Blood & Tissue kit, then sonicated using a Covaris M220 Focused-ultrasonicator, following the manufacturers’ instructions. Then the genomic DNA was sent to UCLA TCGB core to conduct the WGBS library construction and sequencing.

first: Li

last: Yan-Ruide

first: Zhu

last: Yichen

last: Zhe

last: Shuo

first: Zhou

last: Xianghong

first: Yang

last: Lili


first: Yichen

last: Zhu

state: California

address: 610 Charles E Young Drive S

institute: University of California, Los Angeles

overall_design: Gene expression profiling of therapeutic cells products including MCAR-T, PBMC-MCAR-NKT-IL15, PBMC-NK, and Allo15MCAR-NKT (Re-analysed Samples from PRJNA1128571/GSE270820: MCAR-T---GSM8352657, Allo15MCAR-NKT---GSM8352672; and PRJNA1299401/GSE304213: PBMC-MCAR-NKT-IL15---GSM9145254)

first: Yan-Ruide

first: Lili

last: Yang


title: Highly active chromosome regions preferentially associate with two perispeckle networks that partition the interchromatin space (TSA-seq)

city: Boston

last: DCIC

state: MA

address: 10 Shattuck St

institute: 4D Nucleome - Data Coordination and Integration Center

summary: A subset of highly active chromosomal "hot zones" reproducibly positions adjacent to nuclear speckles (NS). Genes within these regions amplify their expression with NS proximity. However, gene expression changes inversely correlate with changes in NS distance genome-wide. We hypothesized the existence of additional gene expression "niches" away from but spatially correlated with NS.  Here we report the identification of two dynamic perispeckle patterns of protein concentrations extending outwards from nuclear speckles and persisting even after NS are eliminated. Highly active chromosome regions which weakly associate with NS instead show close, NS-independent association with these perispeckle patterns.  Additionally, transcripts from model intron-containing versus intronless genes associate differentially with these two patterns. While genes within speckle-associated genomic regions predominately are downregulated upon nuclear speckle depletion, genes associated with perispeckle patterns are biased towards upregulation. We suggest the interchromatin space (ICS) is partitioned into additional gene expression “niches”- surrounding and extending from nuclear speckles- that may be involved in mRNA and gene dynamics.

overall_design: Total 44 samples generated using TSA-seq in Homo sapiens on HCT116 (with anti-THRAP3 or anti-DDX39B or anti-SON treated with Auxin or DMSO) and U2OS (with anti-DDX39B, anti-THRAP3, anti-SON) cell lines.

first: Neha

last: Chivukula Venkata

first: Jiah

last: Kim

first: Gabriel

last: Faber

first: Saireet

last: Misra

first: Atabek

last: Bektash

first: Pankaj

last: Chaturvedi

first: Gabriela

last: Hernandez

first: Joseph

last: Dopie

first: Masato

last: Kanemaki

first: Kyu

last: Young Han

first: Yaron

last: Shav-Tal

first: Andrew

last: S Belmont


title: Connexin 43 Suppression Enhances Contractile Force in Human iPSC-derived Cardiac Tissues

city: Tokyo

first: Takuma

last: Takada

address: 8-1, Kawada-cho, Shinjuku-ku

country: Japan

institute: Tokyo Women's Medical University

summary: Connexin 43 (Cx43) plays a crucial role in maintaining synchronous contraction in the heart. However, it remains unclear whether Cx43 directly influences the contractile force and synchrony of entire cardiac tissues. Previously, we successfully developed human-induced pluripotent stem cell (hiPSC)-derived cardiac tissues capable of directly measuring both the contractile force of the entire tissue and cellular synchrony within it. This study aimed to evaluate whether regulating GJA1, the gene encoding Cx43, could enhance contractility and synchrony in these tissues. Using adeno-associated virus (AAV), we mediated GJA1 overexpression (OE) or knockdown (shGJA1) in bioengineered hiPSC-derived cardiac tissues. Under electrical stimulation at 60 ppm, there were no significant differences in contractile force between the AAV-GJA1-OE and control tissues (0.78 ± 0.39 vs. 0.98 ± 0.43 mN, p = 0.32). Synchrony levels were also similar between these groups (p = 0.20). In contrast, shGJA1 tissues demonstrated significantly higher contractile force compared to scramble controls (1.55 ± 0.38 vs. 1.20 ± 0.15 mN, p = 0.039), although the difference in synchrony was not statistically significant (p = 0.08). RNA sequencing data revealed that a total of 37,199 genes were detected, comparing AAV6-GFP control and GJA1-OE treated hiPSC-CMs, as well as AAV6-shRNA scramble and shGJA1 treated hiPSC-CMs. We highlighted several candidate genes potentially contributing to the enhanced contractile force observed in the shGJA1 group. Furthermore, nineteen common genes were identified between the upregulation of shGJA1 compared to scramble and downregulation of GJA1-OE compared to control, which were associated with cell proliferation, transcription, contraction, and BMP signaling pathways. In conclusion, Cx43-OE did not appear to influence contractility and synchrony, meanwhile, Cx43 suppression may effectively improve contractility without impairing the synchrony in the entire cardiac tissues. Cx43 expression beyond a certain threshold may be sufficient to maintain synchronous contraction in the tissues.

overall_design: AAV serotype 6-mediated regulation of the GJA1 gene in hiPSC-derived cardiac tissue We employed an AAV serotype 6 vector to mediate GJA1 overexpression (OE), knockdown (shGJA1), and GCaMP expression in bioengineered hiPSC-derived cardiac tissues. Viral particles containing the AAV serotype 6 vector were constructed to express GJA1 and EGFP genes linked by a T2A sequence (AAV-GJA1-T2A-GFP), or EGFP alone, driven by the cytomegalovirus (CMV) promoter. The following vectors were constructed and packaged by VectorBuilder (Santa Clara, CA): pAAV[Exp]-CMV>EGFP:WPRE (VB010000-9394npt), pAAV[Exp]-CMV>hGJA1[NM_000165.5](ns):T2A:EGFP: WPRE (VB900089-0611jqt), pAAV[shRNA]-EGFP-U6>Scramble_shRNA (VB010000-0023jze), pAAV[shRNA]-EGFP-U6>hGJA1[shRNA#1] (VB900137-4392ndg), and pAAV[Exp]-CMV>GCaMP6f:WPRE (VB220427-1461cuw). Vector IDs can be used to retrieve additional information about these vectors on vectorbuilder.com.

first: Katsuhisa

last: Matsuura

first: Tatsuro

last: Iida

first: Toshiharu

last: Koike

first: Hidekazu

last: Sekine

first: Yuhei

last: Higashi

first: Tsukasa

last: Hara

first: Daisuke

last: Sasaki

first: Kyohei

last: Fujita

first: Yuto

last: Hinata

first: Junichi

last: Yamaguchi

first: Tatsuya

last: Shimizu


title: Orientia tsutsugamushi modulates p53, the cell cycle, and genotoxicity to maintain its intracellular niche

city: Richmond

first: Paige

last: Allen

state: VA

address: 1220 East Broad MMRB 4-055

department: Microbiology and Immunology

institute: Virginia Commonwealth University

summary: Infections by intracellular pathogens often cause insult to host cell DNA, which stimulates responses that ultimately eliminate the damaged cell and hence the microbial niche. p53 is an innate immunity mediator that responds to DNA damage and intracellular infection by transcriptionally activating pathways that arrest the cell cycle, repair DNA, and elicit apoptosis. How pathogens counter p53 are incompletely understood. Here, we demonstrate that the endotheliotropic obligate intracellular bacterium Orientia tsutsugamushi blocks transcription of TP53 to nearly deplete p53 levels. Contrary to the unrestricted proliferation expected based on the transcriptome of p53-deficient infected cells, Orientia arrests the cell cycle at S phase to promote bacterial replication. It protects host endothelial cells from DNA damage even if induced by etoposide and delays genotoxic-dependent apoptosis until late in infection once a high bacterial load has been achieved. TP53 downregulation, protection against genotoxicity, and inhibition of DNA damage-dependent apoptosis are executed by the Orientia nucleomodulatory effector, Ank13. Therefore, O. tsutsugamushi inhibits TP53 expression and genotoxicity to reconfigure the intracellular environment of its host cell into one that favors bacterial replication.

overall_design: RNAseq profiling of O. tsutsugamushi infected endothelial cells compared to uninfected cells across the replication cycle.

first: David

last: Armistead

first: Svetlana

last: Blinova

first: Jason

last: Carlyon


title: DNA methylation patterns associated with prior tuberculosis infection in people with HIV

city: Kampala

first: Joseph

middle: Baruch

last: Baluku

address: Mulago Hill Rd

country: Uganda

institute: Makerere University Lung Institute

type: Methylation profiling by genome tiling array

summary: Background: Mechanisms by which prior tuberculosis (TB) increases long-term risk for cancer, cardiovascular, and neurological disorders remain unclear, particularly in people with HIV (PWH). This study investigated DNA methylation (DNAm) patterns and associated pathways in PWH with and without prior TB infection.  Methods: DNAm was analyzed in blood samples from 30 PWH (10 with prior latent TB infection [LTBI], 10 with previous successfully treated active TB, and 10 with no TB) using the Illumina MethylationEPIC BeadChip covering over 850,000 CpG sites. Epigenetic age was estimated, and age acceleration was calculated. Differentially methylated CpGs (dmCpGs) and regions (DMRs) were identified, and functional enrichment analyses for Gene Ontology, KEGG pathways, PANTHER database, and gene set enrichment analysis (DisGeNET, dbGaP) were performed. Statistical significance was set at a false discovery rate (FDR) of <0.05.  Results: PWH exhibited significant epigenetic age acceleration, with a mean of 19.32 ± 10.82 years greater than chronological age. This accelerated aging was more pronounced in individuals with any prior TB infection (21.60 ± 12.03 years) compared to those without TB (17.42 ± 9.38 years). In the prior active TB vs. no TB comparison, 7,461 dmCpGs were identified, corresponding to 150 DMRs (p<0.05), with top associated genes including GRAMD1C (hypomethylation), DPP6 (hypermethylation), and HDAC4 (hypomethylation). In the LTBI vs. no TB comparison, 8,598 dmCpGs were observed, corresponding to 39 DMRs (p<0.05), associated with genes such as PLEKHG5 (hypermethylation), STK32C (hypermethylation), and SPATC1L. When comparing any prior TB (active or latent) to no TB, 71,774 dmCpGs and 14 DMRs were identified, including genes like PLEKHG5, KCNN3, and BRSK2. Pathway analyses of prior TB (active or latent) vs. no TB revealed enrichment in neurogenesis, neuron differentiation, axon guidance, and neuroactive ligand signaling. Additional enriched pathways included those related to platelet activation, vascular muscle contraction, and chemokine signaling. Cancer-related pathways such as proteoglycans in cancer, small cell lung cancer, prostate cancer, breast cancer, hepatocellular carcinoma, and thyroid cancer were also enriched. PANTHER analysis showed consistent enrichment in the Wnt signaling pathway and inflammation-mediated pathways across compared groups. DisGeNET analysis linked prior TB DNAm patterns to lymphoid leukemia, while dbGaP analysis identified associations with phenotypes like asthma, body mass index, tunica media, and lymphocyte count  Conclusion: Prior TB infection in PWH is associated with distinct DNAm changes in pathways related to neural function, cardiovascular health, and cancer risk, and is linked to more pronounced epigenetic age acceleration, suggesting epigenetic mechanisms for TB-related long-term complications.

overall_design: We aimed to profile the genomic DNA methylome of people living with HIV (PWH) using a cross sectional epigenomic approach to explore the potential impact of prior tuberculosis (TB) infection on DNA methylation (DNAm) patterns in this study group. Plasma genomic DNA was analyzed using the Infinium Methylation EPICv2 array in a cohort of 10 Latent TB infected individuals, 10 prior Active TB infected individuals , and 10 individuals with no evidence of TB infection.

last: Baruch Baluku

first: Sharon

last: Namiiro

first: Daphine

last: Kigongo

first: Brenda

last: Namanda

first: Hakiimu

last: Kawalya

first: Irene

last: Najjingoa

first: Waiswa

last: Geoffrey

first: Nixon

last: Niyonzima

first: Naghib

last: Bogere

first: Edwin

last: Nuwagira

first: Joshua

last: Rhein

first: Nick

last: Jones

first: Christian

last: Kraef

first: Megan

last: Shaughnessy

first: Arohi

last: Chauhan

first: Immaculate

last: Nankya

first: Sayoki

last: Mfinanga

first: Stanton

last: Gerson

first: Bruce

last: Kirenga


title: Highly active chromosome regions preferentially associate with two perispeckle networks that partition the interchromatin space (RNA-seq)

last: DCIC

overall_design: Total 6 samples generated using RNA-Seq in Homo sapiens on HCT116, (16h Auxin and DMSO control) samples

first: Neha

last: Chivukula Venkata

first: Jiah

last: Kim

first: Gabriel

last: Faber

first: Saireet

last: Misra

first: Atabek

last: Bektash

first: Pankaj

last: Chaturvedi

first: Gabriela

last: Hernandez

first: Joseph

last: Dopie

first: Masato

last: Kanemaki

first: Kyu

last: Young Han

first: Yaron

last: Shav-Tal

first: Andrew

last: S Belmont


title: Chemically modified tRNA enhances the translation capacity of mRNA rich in cognate codons [RNA-Seq]

city: Beijing

first: Jiayu

last: Wang

state: Beijing

address: 38 Xueyuan Rd , Haidian District,Beijing,China

department: School of Pharmaceutical Sciences

institute: Peking University Health Science Center

summary: Although messenger RNA (mRNA) vaccines have been employed to prevent the spread of COVID-19, they are critically limited by instability and low translation capacity. Alterations in tRNA abundance and modification, associated with codon optimality, impact mRNA stability and protein output in a codon-dependent manner, implying tRNA as a potential translation enhancer. Here, we report a strategy named tRNA-plus to augment translation based on artificially modulating the tRNA availability. We demonstrated that overexpression of specific tRNAs enhanced the stability and translation efficiency of SARS-CoV-2 Spike mRNA, resulting in substantial improvements in protein levels by up to 4.7-fold. In addition, chemically synthesized tRNAs bearing multiple site-specific modifications, particularly at the anticodon loop and TΨC-loop, exhibited an average of ~4-fold higher decoding efficacy than unmodified tRNA, along with increased stability and reduced immune toxicity. We further leveraged an optimized lipid nanoparticles (LNP) system for codelivery of Spike mRNA vaccine and tRNA, which elicited enhanced spike-specific humoral and cellular immune responses in vivo. The methods presented here may become a general approach for elevating mRNA translation potency, which can be applied to various translation-based fields.

overall_design: mRNA-seq profiling of HEK293T-EF1α-mCherry (WT) cells and their tRNA overexpression derivatives HEK293T-EF1α-mCherry-7SK-tRNALeuCAG (tL) and HEK293T-EF1α-mCherry-7SK-tRNAAlaGGC (tA).

first: Liangzhen

last: Dong


title: Mechanistic and Epigenetic Partitioning of Lamina-Associated Chromatin Revealed by a Genome-Wide Imaging Screen

city: Philadelphia

first: Ricardo

last: Linares Saldana

state: PA

address: 3400 civic center blvd

institute: University of Pennsylvania

summary: The nuclear periphery is a key site for heterochromatin organization in eukaryotic cells, where lamina-associated domains (LADs) promote transcriptional repression and genome stability. Despite their importance, the mechanisms governing LAD positioning in human cells remain poorly understood. To this end, we performed a genome-wide imaging-based screen and identified 101 genes critical for perinuclear LAD localization, with a significant enrichment for RNA-binding proteins. Among these, hnRNPK emerged as a key regulator, required for the perinuclear positioning of approximately 70% of LADs genome-wide. Loss of hnRNPK led to their repositioning away from the nuclear periphery without altering global heterochromatin state, yet resulted in misexpression of genes within these domains. Notably, hnRNPK-sensitive LADs are uniquely enriched for H3K27me3, distinguishing them from hnRNPK-insensitive LADs that are predominantly marked by H3K9me3. These findings reveal mechanistically distinct classes of LADs and suggest that specialized pathways underlie their spatial organization. Our results uncover a pivotal role for hnRNPK in regulating chromatin architecture and highlight the broader diversity of LAD tethering mechanisms.

overall_design:
LB1, H3K9me2, H3K9me3, and H3K27me3 ChIP-seq in HCT116 cells in control and HNRNPK knockdown.
Bulk RNA-seq in HCT116 cells in control and HNRNPK knockdown.

first: Patrick

last: Walsh

first: Elizabeth

middle: B

last: Kraeutler

last: Linares-Saldana

first: May

last: Wai

first: Shuo

last: Zhang

first: Son

middle: C

last: Nguyen

first: Parisha

last: Shah

first: Daniel

last: Park

first: Haris

last: Muzaffar

first: Rajan

last: Jain

first: Eric

middle: F

last: Joyce


title: Variation at the R181 residue of p53 confer loss of p53 DNA binding cooperativity with the retention of mitochondrial-associated apoptosis

first: Kara

last: Maxwell

address: 421 Curie Blvd

summary: The p53 tumor suppressor binds DNA cooperatively as a tetramer, mediated by salt-bridge interactions between p53 residues E180 and R181. Variants at the R181 residue are one of the most commonly identified TP53 pathogenic variants by germline genetic testing. We show that families with TP53 p.R181H and p.R181C variants show an attenuated cancer risk phenotype compared to patients with classic Li Fraumeni Syndrome due to hotspot loss of function variants. Despite this phenotype, we find that p53 R181H and R181C variants have reduced ability to bind to p53 promotor target sequences and transactivate p53 target genes.  We further show that p53 R181H and R181C retain wild-type p53 structure and tetramerization. In addition, R181-mutant cells undergo apoptosis through wild-type p53 activity at the mitochondria. These results indicate that retention of transcription-independent p53 tumor suppressor function may result in a reduced penetrance cancer risk syndrome in humans.

overall_design: RNA-sequencing of cancer cell lines (HCT116 colorectal and MCF7 breast cancer lines) CRISPR-engineered at the TP53 locus for the genotypes: TP53 +/-, TP53 R181H/-, and TP53 R181C/-. Triplicates of each cell type were cultured in a Nutlin-3a drug timecourse (Nutlin-3a activates TP53 pathways) for 0 hours (DMSO-treated), 8 hours, and 24 hours. RNA-seq was performed on each replicate for each sample to observe if the mutant p53 cell lines were able to induce p53 target genes after Nutlin-3a treatment.

first: Renyta

last: Moses

first: Ryan

last: Hausler


title: Integrative Clonal Tracing and CRISPR Screening Identify Temporal and Microenvironmental Determinants in Ovarian Cancer Metastasis

city: Dallas

first: Siyuan

address: 6001 Forest Park Rd

department: Department of Pathology

institute: UT Southwestern Medical Center

summary: We used scRNA-seq (10x Genomics) coupled with CITE-seq based HTO labeling to profile and compare transcriptomes of omentums and ascital fluid harvested from naive or metastasis bearing wild type C57Bl/6 mice. There are three samples from different animals (M-HTOs) that were pooled for loading onto one 10x Chromium lane + eight samples/M-HTOs pooled for a second lane. Later, three seperate libraries were prepared from each 10x lane: HTO, cell barcode (LARRY), and transcriptome. Within the cell barcode libraries: BC.ID1, BC.ID2, BC.ID3, BC.ID4, BC.ID5 and BC.ID6 are used to distinguish different timepoints of injection - early, mid, and late seeding in descending order (meaning BC.ID6 was earliest timepoint, BC.ID1 is latest timepoint).

overall_design: Omentums and lavage/ascital fluid were obtained from naive and metastasis-bearing female C57Bl/6 mice. Omental metastases were established by repeated injection of 400K cell/dose (6x times) of barcoded ID8 p53-/- cells over 12 days, followed by 4 weeks of tumor outgrowth time. We stained each sample with it's own unique hashing antibody so that we could subsequently pool the samples for loading onto two lanes on the 10x Chromium machine and later prepare 2x three libraries consisting of those samples.

first: Emilja

last: Aleksandrovic


title: Highly active chromosome regions preferentially associate with two perispeckle networks that partition the interchromatin space.

last: DCIC

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

overall_design: Refer to individual Series


title: Chemically modified tRNA enhances the translation capacity of mRNA rich in cognate codons [Ribo-Seq]

first: Jiayu

last: Wang

overall_design: Ribo-seq profiling of HEK293T-EF1α-mCherry (WT) cells and their tRNA overexpression derivatives HEK293T-EF1α-mCherry-7SK-tRNALeuCAG (tL) and HEK293T-EF1α-mCherry-7SK-tRNAAlaGGC (tA) transfect with Spike plasmid.

first: Liangzhen

last: Dong


title: Chemically modified tRNA enhances the translation capacity of mRNA rich in cognate codons [ncRNA-Seq]

type: Non-coding RNA profiling by high throughput sequencing

overall_design: tRNA-seq profiling of HEK293T-EF1α-mCherry (WT) cells and their tRNA overexpression derivatives HEK293T-EF1α-mCherry-7SK-tRNALeuCAG (tL)


title: Graphene Optoelectronics for Non-Genetic Neuromodulation in Disease Modeling, Stem Cell Maturation, and Biohybrid Robotics

city: San Diego

first: Elena

last: Molokanova

address: 9500 Gilman Drive

institute: NeurANO Bioscience

summary: Light can serve as a tunable trigger for neurobioengineering technologies, enabling probing, control, and enhancement of brain function with unmatched spatiotemporal precision. Yet, these technologies often require genetic or structural alterations of neurons, disrupting their natural activity. Here, we introduce the Graphene-Mediated Optical Stimulation (GraMOS) platform, which leverages graphene’s optoelectronic properties and its ability to efficiently convert light into electricity. Using GraMOS in longitudinal studies, we found that repeated optical stimulation enhances the maturation of hiPSC-derived neurons and brain organoids, underscoring GraMOS’s potential for regenerative medicine and neurodevelopmental studies. To explore its potential for disease modeling, we applied short-term GraMOS to Alzheimer’s stem cell models, uncovering disease-associated alterations in neuronal activity. Finally, we demonstrated a proof-of-concept for neuroengineering applications by directing robotic movements with GraMOS-triggered signals from graphene-interfaced brain organoids. By enabling precise, non-invasive neural control across timescales from seconds to weeks, GraMOS opens new avenues in neurodevelopment, disease treatment, and robotics.

overall_design: RNA seq analysis of hIPSC-derived 4 month old WT83 organoids treated with reduced graphene oxide and light stimulation

first: Alex

last: Savchenko


title: Targeting cancer-associated fibroblast-mediated LIF/LIFR axis improves the therapeutic efficacy of gemcitabine and nab-paclitaxel in pancreatic cancer

city: Omaha

first: Sushil

last: Kumar

state: NE

address: 985870 Nebraska Medical Center, DRC1

department: Biochemistry and Molecular Biology

institute: UNMC

summary: Pancreatic ductal adenocarcinoma (PDAC) responds poorly to chemotherapeutics due to inherent drug resistance orchestrated by crosstalk between cancer cells and cancer-associated fibroblasts (CAFs). The LIF/LIFR axis activated by this crosstalk contributes significantly to cancer cell stemness and is a potential therapeutic target. Combined targeting of LIFR with small molecular inhibitors along with standard of care remains unexplored.The efficacy of LIFR small molecule inhibitor, EC359 was evaluated in combination with standard-of-care using human and mouse cell lines, tumoroids, KPC (KrasG12D; TP53R172H; Pdx1-Cre), and orthotopically co-implanted murine models. The impact of LIFR targeting on PDAC was analyzed by RNA-sequencing, immunohistochemistry, western blot, and immune profiles by flow cytometry.In co-implantation murine models, EC359 (5mg/kg body weight), in combination with gemcitabine (Gem, 25mg/kg body weight), reduced the tumor burdens up to 90% compared to the untreated controls (p<0.001) and by 55% compared to Gem alone. The RNA-seq analysis of treated tumors showed significant alterations in stemness markers, extracellular matrix modulation, microtubule structure assembly, and adaptive immune response, suggesting the simultaneous targeting of cell-intrinsic and TME-mediated mechanisms by EC359. The EC359 in autochthonous KPC tumors improved the efficacy of Gem and nab-paclitaxel targeting, increased the dendritic cells, but reduced regulatory T-cells, systemically. Mechanistically, EC359 reduces the PDAC cell stemness, stabilizes the microtubule assembly, and reduces the immunosuppressive microenvironment, contributing to improved efficacy of standard of care in PDAC.

overall_design: RNA-seq data of orthopically co-implanted PCCs and CAFs (1:1 ratio) in  C57BL/6 (KCT3266:mCAFs) mice. After the tumors were palpable, animals were treated with vehicle, EC359 (E), Gem (G), and E+G.

first: Rakesh

last: Bhatia

first: Imran

last: Khan

first: Xiaoqi

last: Li

first: Shailendra

last: Gautam

first: Parthasarathy

last: Seshacharyulu

first: Zahraa

middle: W

last: Alsafwani

first: Namita

last: Bhyravbhatla

first: Moorthy

last: Ponnusamy

first: Maneesh

first: Mokenge

last: Malafa

first: Santhamma

last: Bindu

first: Ahmed

last: Gulzar

first: Hareesh

last: Nair

first: Surinder

middle: K

last: Batra


title: CRISPR-Cas9 Screening Reveals Microproteins Regulating Adipocyte Proliferation and Lipid Metabolism [RNA-seq]

first: April

middle: Elizabeth

last: Williams

address: 10010 N Torrey Pines Rd

department: IGC

institute: Salk Institute for Biological Studies

summary: Small open reading frames (smORFs) encode microproteins that play crucial roles in various biological processes, yet their functions in adipocyte biology remain largely unexplored. In a previous study, we identified thousands of smORFs in white and brown adipocytes derived from the stromal vascular fraction (SVF) of mice using ribosome profiling (Ribo-Seq). Here, we expand on this work by identifying additional smORFs related to adipocytes using the in vitro 3T3-L1 preadipocyte model. To systematically investigate the functional relevance of these smORFs, we designed a custom CRISPR/Cas9 guide RNA (sgRNA) library and screened for smORFs influencing adipocyte proliferation and differentiation. Through a dropout screen and fluorescence-assisted cell sorting (FACS) of lipid droplets, we identified dozens of smORFs that regulate either cell proliferation or lipid accumulation. Among these, we validated a novel microprotein as a key regulator of adipocyte differentiation. These findings highlight the potential of CRISPR/Cas9-based screening to uncover functional smORFs and provide a framework for further exploration of microproteins in adipocyte biology and metabolic regulation.

overall_design: Riboseq and RNA seq profiling of undifferentiated and differentiated 3T3-L1 Cells. 3T3-L1 cells are induced to differentiate into mature adipoctes through adding a cocktail containing insulin, IBMX, and dexamethasone. Differentiated adipocytes were collected at Days 3 and 7.

first: Victor

last: Pai

first: Alan

last: Saghatelian


title: The effect of LIG (ligustilide) on gene expression in LX-2 cells.

first: Li

last: xiaojiaoyang

address: Bei jing shi chao yang qu bei san huan dong lu 11

institute: Beijing University of Chinese Medicine

summary: We performed gene expression profiling analysis using data obtained from RNA-seq of LX-2 cells treated with TGF-β or TGF-β + LIG.

overall_design: Compare gene expression of LX2 cells transfected with 5 μg/mL TGF-β or 5 μg/mL TGF-β + 20 μM LIG. Each group had three replicates.


title: CRISPR-Cas9 Screening Reveals Microproteins Regulating Adipocyte Proliferation and Lipid Metabolism [Ribo-seq]


title: Vitamin D Enhances Antiviral Responses in Dengue Virus-Infected Macrophages by Modulating Early-Response Gene Expression

city: Medellin

first: Yordi

middle: Sebastián

last: Tamayo Molina

state: Antioquia

country: Colombia

institute: University of Antioquia

summary: Dengue virus (DENV), the etiological agent of dengue fever, remains a global health concern, leading to severe illness and death in the absence of any definitive cure. Research has shown that vitamin D may reduce DENV replication in vitro and that dengue patients with low or deficient vitamin D levels are at higher risk of severe dengue. Studies indicate that viral replication is inhibited in human monocyte-derived macrophages (MDM) differentiated in the presence of vitamin D (D3MDM), suggesting that vitamin D may prevent DENV entry into host cells. However, despite these findings, the role of vitamin D in regulating the temporal expression patterns of genes as early, mid, and late transcriptional profile of DENV-infected macrophages remains unclear. Therefore, utilizing a kinetic transcriptomic profile is crucial. This approach provides detailed insights into the dynamic changes in gene expression over time, helping to clarify how vitamin D can modulate the immune response at critical stages of DENV infection. To address the transcriptional dynamics, we conducted a comprehensive analysis of gene expression patterns in MDM and D3MDM infected with Dengue virus serotype 2 (DENV-2). Utilizing bulk RNA sequencing alongside a standard viral growth curve, we systematically analyzed transcriptional kinetics by selecting key time points: 1.5, 3, 5.5, and 10 hours post-infection (h.p.i.) to monitor early viral entry and replication events and 24 h.p.i. to assess gene expression during peak viral particle production. Our temporal analysis revealed a progressive increase in cellular transcripts within the first hour of infection, with a more pronounced gene expression pattern in DENV-2-infected MDM compared to DENV-2-infected D3MDM at this early stage. Enrichment analysis indicated a reduced inflammatory response in DENV-2-infected D3MDM. Additionally, transcription factor analysis suggested diminished NF-κB signaling, but enhanced IRF5 activity was elevated in the DENV-2-infected D3MDM. High-dimensional clustering analysis identified nine unique gene clusters across both macrophage types, with notable upregulation of genes associated with antiviral activity, including IDO1, ISG20, OASL, IFI44L, RSAD2, IFIT1, MX1, EPSTI1, CXCL10, and CXCL11 in DENV-2-infected D3MDM at 1.5 h.p.i., suggesting an enhanced early antiviral response. These findings indicate that vitamin D modulates the magnitude and diversity of the early transcriptional responses, highlighting its potential as a therapeutic option to mitigate DENV severity.

overall_design: Monocytes-derived macrophages in precense or absence of vitamin D [0.1nM] were infected with DENV2 new guinea strain at MOI of 5. Cells were collected at 1.5-, 3-, 5.5-, 10- and 24-hour post-infection.


title: Spatial Transcriptomics Reveals Inhba/Smad2/E2f4 Axis in Lrp2high Thecal Cell Proliferation in Androgen-Induced PCOS Mice

city: Zhengzhou

first: Man

last: Luo

address: 195 Tongbai Road, Zhongyuan District

institute: Zhengzhou Central Hospital Affiliated to Zhengzhou University

summary: Hyperandrogenemia is a primary character of polycystic ovary syndrome (PCOS), a leading cause of woman infertility. As a source of androgen secretion, thecal cells (TC) exhibit hyperplasia in the ovarian of PCOS conditions providing a potential mechanism for hyperandrogenemia. However, the molecular events driving TC hyperproliferation are not fully elucidated. In this study, we employed spatial transcriptomics investigating the ovarian of a mouse PCOS model induced by dehydroepiandrosterone (DHEA). Substantial alteration was observed in gene expression across multiple cell types in the ovarian, and a dramatic expansion was observed in Lrp2high subpopulation of TC. Functional analysis of gene interaction led to identification of the Inhba/Smad2/E2f4 pathway in the hyperproliferation of Lrp2high subset. Knockdown of any gene in the pathway led to suppression of TC proliferation, with a dominant impact upon Inhba inactivation. These results suggest that the Inhba/Smad2/E2f4 axis may be responsible for TC over proliferation in PCOS and a potential therapeutic target in the control of PCOS.

overall_design: 25-day-old female ICR mice were purchased from Liaoning Changsheng Biotechnology Co., Ltd and housed under controlled conditions (12-hour light/dark cycle, temperature 22 ± 2°C) with free access to food and water. DHEA was dissolved in 10% sesame oil (in 95% ethanol) and administered daily to each mouse in the model group at 6 mg/100 g body weight in 0.1 mL for 20 days. Control mice were injected with vehicle in the same way.


title: Notch-activated basophils support intestinal CD4+ T cell fate and function during helminth infection

city: Seattle

first: Elia

last: Tait Wojno

state: WA

address: 750 Republican Street

department: Immunology

institute: University of Washington

summary: Helminth infections affect billions of people worldwide and cause substantial morbidity.  Intestinal helminth infection provokes Type 2 inflammation orchestrated by CD4+ T  helper 2 (Th2) cells. Th2s produce interleukin (IL)-4 and IL-13 that prompt an epithelial  “weep and sweep” response to drive parasite clearance. Tissue-specific cues optimize  CD4+ T cell responses, but the mechanisms regulating intestinal Th2 responses  remain unclear. Previously, we identified that the Notch signaling pathway in basophils,  rare granulocytes, drove effective parasite clearance and an optimal Th2 response  during Trichurismuris infection, a mouse model of human whipworm. Here we report  basophil-intrinsic Notch was required for infection-elicited Th2 cytokine responses and  a broader IL-4 production program across intestinal CD4+ T cell subsets. In vitro,  basophils supported CD4+ T cell cytokine production in a contact-dependent manner,  independent of basophil-secreted factors, and was dependent on autocrine IL-4  production from CD4+ T cells. In vivo, basophil-intrinsic Notch mediated basophil-Th2  cell interactions in the cecum during infection. Thus, Notch-programmed basophils act  in a contact-dependent manner to optimize intestinal CD4+ T cell function during  helminth infection. These findings improve our understanding of the tissue-specific  mechanisms regulating intestinal CD4+ T cell responses at inflamed mucosal barriers  during Type 2 immunity.

overall_design: Bulk RNA-seq of cecum CD4+ T cells from Mcpt8-Cre- and Mcpt8-Cre+ DNMAMLF/F mice at steady state or during T. muris infection.

first: Lindsey

last: Warner

first: Eric

last: Helm


title: Decoding the Amniotic Membrane Transcriptome during Equine Ascending Placentitis

city: COLLEGE STATION

first: Yatta

last: Boakari

state: TX

address: 500 RAYMOND STOTZER PKWY

department: VLCS

institute: TEXAS A&M UNIVERSITY

summary: The equine amniotic membrane is a critical barrier to the amniotic compartment and may contribute to surfactant synthesis. To investigate its role in ascending placentitis, we used RNA sequencing, bioinformatics, and immunohistochemistry to analyze gene expression in amniotic membranes from experimentally induced placentitis cases (n = 6) and gestationally matched controls (n = 6). We identified 288 differentially expressed genes (DEGs), with upregulation of TLR4, PTGS2, PTGES, MMP9, CASP3, SOD2, BNIP3, and HMOX1 in placentitis. Immunohistochemistry confirmed protein expression of TLR4 and PTGS2. Functional annotation revealed enrichment in toll-like receptor signaling, suggesting immune activation may impair placental function. These findings highlight the amniotic membrane’s active role in immune response during placentitis.

overall_design: RNAseq profiling of the aniotic membrane of mares during ascending placentitis compared to a negative control.

first: Sophia

last: Marchio

first: Matthew

last: Scott


title: Transposable elements are dynamically expressed within medium spiny neurons and associated with molecular and behavioral adaptations to cocaine [scRNA-seq]

first: Gabriella

last: Silva

address: 1217 Marshall Street

summary: A more complete understanding of the molecular mechanisms by which substance use is encoded in the brain could illuminate novel strategies to treat substance use disorders, including cocaine use disorder (CUD). We have previously discovered that Zfp189, which encodes a Krüppel-associated box zinc finger protein (KZFP) transcription factor (TF), differentially accumulates in nucleus accumbens (NAc) Drd1+ and Drd2+ medium spiny neurons (MSNs) over the course of cocaine exposure and is causal in producing MSN functional and behavioral changes to cocaine. Here, we aimed to illuminate the brain cell-type specific molecular mechanisms through which this KZFP TF produces chronic cocaine -related brain changes, with emphasis on investigating transposable elements (TEs), since KZFPs like ZFP189 are known regulators of TEs. We discovered that expression of NAc TE transcripts was dramatically increased by cocaine experience, the most sensitive NAc cell-type was MSNs, and TEs in Drd1+ MSNs were considerably more dynamic over the course of cocaine exposure than TEs in Drd2+ MSNs. We demonstrated that synthetic ZFP189VPR is capable of dysregulating NAc TEs. In our snRNAseq data we observed that, relative to ZFP189WT, NAc manipulated with ZFP189VPR impeded cocaine-induced gene expression in NAc cell-types, including both Drd1+ and Drd2+ MSNs. Within either MSN subtype, the consequence of normal ZFP189 function was to enhance immune-related gene expression, and ZFP189VPR impeded these gene expression profiles. We discovered that behavioral and cell morphological adaptations to cocaine are produced by dysregulating TEs with ZFP189VPR in Drd1+ MSNs or stabilizing TEs with ZFP189WT in Drd2+ MSNs, revealing a persistent opponent process balanced across MSN subtypes and weighted by TE stability and consequent gene expression within MSN subtype.

overall_design: RNA-seq of mouse Nac brain punches that have been virally infected with HSV's containing synthetic ZFP189 transcription factors: ZFP189WT, ZFP189VPR, ZFP189NFD.These Mice Received 3 days of cocaine injections.

first: Amber

last: Kaplan

first: Celeste

middle: R

last: Park

first: Joseph

middle: A

last: Picone

first: R

last: Kim

first: Rachel

last: Neve

first: Peter

last: Hamilton


title: Tomatidine Attenuates Inflammatory Responses to Exercise-Like Stimulation in Donor-derived Skeletal Muscle Myobundles

city: Orlando

first: Siobhan

last: Malany

state: FL

address: 6550 Sanger Rd

department: Department of Cellular and Systems Pharmacology

institute: UF Research and Academic Center at Lake Nona

summary: We assessed donor-specific response to tomatidine known to inhibit muscle atrophy and promote skeletal muscle hypertrophy. Bioinformatic analyses revealed that infusion of tomatidine during electrical stimulation modulated the IL-6/JAK/STAT3 pathway improving muscle synchronicity in young myobundles compared to those from older volunteers.

overall_design: CD56 myoblasts-derived from young active and old sedentary muscle biopsies, differentiated into functional myobundles, that exhibited classic skeletal muscle bio-functions, were treated with tomatidine. We report on the differences in gene expression  profiling between the treated- vs non-treated young and  old-derived myobundles . A minimum of three biological replicates was used for RNA seq.

first: Maddalena

last: Parafati

first: Tushar S

last: Shenoy

first: Zon

last: Thwin

first: Mauro

last: Parlavecchio


title: The effect of LIG (ligustilide) on gene expression in liver of mice undergoing BDL-induced liver fibrosis.

first: Li

last: xiaojiaoyang

summary: In order to evaluate whether LIG produces the anti-fibrotic effects in the liver,we established BDL-induced liver fibrosis mice model and administered with LIG. Then,  we collected liver tissues and employed RNA-seq analysis.

overall_design: Mice were randomly divided into sham, bile duct ligation (BDL) and BDL + 10 mg/kg LIG. Liver tissues were collected at the end of different treatment. Total liver RNA was extracted and RNA-sequecing was performed.


title: Healthy human induced pluripotent stem cell-derived cardiomyocytes exhibit sex dimorphism even without the addition of hormones

city: MINNEAPOLIS

first: Sophie

middle: E

last: Givens

state: MN

address: 312 Church Street SE, Room 7-256

department: Biomedical Engineering

institute: University of Minnesota

summary: Human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CM) are a valuable cell type for studying human cardiac health and disease in vitro. However, it is not known whether hiPSC-CM display sex dimorphism and therefore whether sex should be incorporated as a biological variable in in vitro studies that include this cell type. To date, the vast majority of studies that utilize hiPSC-CM do not include both male and female sex nor stratify results based on sex because it is challenging to amass such a cohort of cells. Here we generated three female and three male hiPSC-lines from adult left ventricular cardiac fibroblasts as a resource for studying sex differences in in vitro cardiac models. We used this resource to generate hiPSC-CM and maintained them in basal media without exogenous hormones. Functional assessment of CM showed enhanced calcium handling in female-derived hiPSC-CM relative to male. Bulk RNA sequencing revealed over 300 differentially expressed genes (DEG) between male and female hiPSC-CM. Gene ontology analysis of DEG showed distinct differences in pathways related to cardiac pathology including cell-cell adhesion, metabolic processes, and response to ischemic stress. Differential expression of the sodium channel auxiliary unit SCN3B was found and validated through patch-clamp measurements of sodium currents showing increased peak amplitude and window current in female hiPSC-CM. These findings highlight the importance of considering sex as a variable when conducting studies to evaluate aspects of human cardiac health and disease related to cardiomyocyte function.

overall_design: RNA-seq profiling of human induced pluripotent stem cells (hiPSC) that were differentiated into cardioymocytes using small molecule WNT modulation. Three batches from three female and three male hiPSC-lines were sequences.

first: Brenda

last: Ogle

first: Abygail

last: Andebrhan


title: Microbiota promote enhanced CD39 expression in gamma delta (gd) intraepithelial lymphocytes through the activation of TCR and IL-15 signaling.

city: New York

first: Sara

last: Alonso

state: New York

address: 1470 Madison Ave

institute: Icahn School of Medicine at Mount Sinai

summary: Intraepithelial lymphocytes expressing the gd T cell receptor (gd IEL) provide continuous surveillance of the intestinal epithelium. We report that mice harboring a microbiota-specific hyperproliferative gd IEL (gdHYP) phenotype also upregulate the expression of the ectonucleotidase CD39, a marker of regulatory gd T cells. Enhanced TCR and IL-15 signaling correlates with a progression from a naïve-like CD39neg gd IEL to a more mature, tissue-adapted CD39hi IEL population. We find that TCRgd activation drives CD122-mediated CD39 upregulation on gdHYP IELs and increased mucosal IL-15 further amplifies CD39 expression in gdHYP IELs. Notably, CD39 induction requires sustained exposure to the gdHYP-associated microbiota. Increased IL-15 signaling prolongs IEL survival and enhances gdHYP IEL bioenergetic potential. Notably, CD39hi gd IELs produce less pro-inflammatory cytokine, which may explain the lack of histopathology in gdHYP mice. Overall, our study identifies a previously unappreciated mechanism by which an altered microbiota amplifies CD39 expression on gdHYP IELs, leading to the expansion of gd IELs with regulatory potential.

overall_design: RNAseq was performed on sorted Vg7 and Vg1 IELs isolated from murine small intestine from wildtype and gdHYP mice.

first: Karen

last: Edelblum


title: Transposable elements are dynamically expressed within medium spiny neurons and associated with molecular and behavioral adaptations to cocaine

first: Gabriella

last: Silva

first: Amber

last: Kaplan

middle: J


title: miR-210 deletion induces a pro-inflammatory status in murine macrophages and alters their polarization towards the pro-reparatory phenotype

city: Bucharest

first: Laudy

last: Cherry

state: Sector 5

address: Strada B.P.Hasdeu nr.8, sector 5, Bucuresti

department: Biology

country: Romania

institute: Institute of cellular biology and pathology

summary: Background: Macrophages play fundamental roles in immune regulation and tissue homeostasis, serving as one of the primary cell types that orchestrate tissue repair after injury. MicroRNA-210 is a hypoxia-inducible, small non-coding RNA involved in regulating metabolic adaptation and inflammatory responses during normal repair processes. However, its role in macrophage polarization is not fully understood. Here, we report the impact of miR-210 deletion on macrophage polarization towards a pro-reparatory phenotype. Methods: Bone marrow-derived macrophages were obtained from miR-210 knockout (KO) and wild-type (WT) mice and polarized toward the pro-reparative M2 phenotype. The transcriptomic profile of these cells, as well as their phagocytic capacity, cell energy phenotype, and cytokine production, were comparatively assessed to determine the impact of miR-210 on the polarization process of macrophages into the M2-like phenotype. Results: As compared to WT counterparts, miR-210-KO M0 macrophages exhibited reduced glycolytic activity and diminished metabolic flexibility. However, miR-210 KO macrophages exhibited increased phagocytosis in both M0 and M2 states, potentially as an adaptive response to their metabolic limitations. Transcriptomic analysis revealed distinct clustering between the M0 and M2 states, along with several notable differences in the transcriptional patterns between the two genotypes. Analysis of genes with altered expression levels indicated a higher pro-inflammatory state in resting miR-210 KO macrophages compared to WT control cells. These data were further confirmed by higher levels of IL-6 and TNF-α secreted by miR-210 KO M0 macrophages compared to WT cells. Analysis of the biological processes activated during the polarization process towards M2 phenotypes revealed an incomplete polarization of miR-210 KO cells, which was partly a result of a milder activation of essential mitotic regulators, leading to slower cell cycle progression and reduced proliferation. Conclusion: Our data offer new insights into the role of miR-210 in macrophages and their polarization toward the pro-reparatory phenotype. The fine-tuning involvement of miR-210 in immune responses may have potential implications for chronic inflammation, immune dysfunction, and tissue repair.

first: Carmen

last: Neculachi

first: Evelyn

last: Rusu

first: Catalina

last: Colan

first: Sergiu

last: Catrina

first: Maya

last: Simionescu

first: Fabio

last: Martelli

first: Mihai

last: Preda

first: Alexandrina

last: Burlacu


title: Combinatorial Immunotherapeutic Strategies in Liver Cancer

city: SAN DIEGO

first: Yichun

last: Ji

state: ca

address: 9500 Gilman drive BRFII Room1220 Bay C #0864

department: PATHOLOGY

institute: UCSD

summary: Background: Immune checkpoint inhibitors combined with antiangiogenic therapy has become the standard of care for advanced hepatocellular carcinoma, albeit with limited therapeutic benefit. Our previous studies demonstrated the immunomodulatory and antitumor effects of polyIC, a synthetic double-stranded RNA. Here, we compared the efficacy of anti-programmed death ligand 1 (?PD-L1) plus polyIC versus ?PD-L1 plus anti-vascular endothelial growth factor (?VEGF) in primary liver tumor models.Conclusion: This preclinical study identifies polyIC as a better enhancer of ?PD-L1 efficacy than ?VEGF in liver cancer, providing a novel strategy for improving immunotherapy outcomes. Further clinical investigation is warranted.

overall_design: We established a primary liver tumor model using hydrodynamic tail vein injection of Ras/Myc oncogenes. Flow cytometry and gene expression analysis were performed to assess immune profiles across treatment groups. Key factors contributing to antitumor efficacy were explored.

first: Li-chun

last: Lu

first: Hao

last: Zhuang

first: Yingluo

last: Liu

first: Yiming

last: Gao

first: Andre

last: Qin

first: Jin

last: Lee

first: Gensheng

last: Feng


title: Therapeutic Targeting of the p300/CBP Bromodomain Enhances the Efficacy of Immune Checkpoint Blockade Therapy

city: lexington

first: Jinghui

state: KY

address: Room 352, HEALTHY KENTUCKY RESEARCH BUILDING, 760 Press Avenue

institute: University of Kentucky

summary: Blockade of immune checkpoints, such as programmed death-ligand 1 (PD-L1), has shown promise in cancer treatment; however, clinical response remains limited in many cancer types. Our previous research demonstrated that p300/CBP mediates the acetylation of the PD-L1 promoter, regulating PD-L1 expression. In this study, we further investigated the role of the p300/CBP bromodomain in regulating PD-L1 expression using CCS1477, a selective bromodomain inhibitor developed by our team. We found that the p300/CBP bromodomain is essential for H3K27 acetylation at PD-L1 enhancers. Inhibiting this modification significantly reduced enhancer activity and PD-L1 transcription, including exosomal PD-L1, which has been implicated as key contributors to resistance against PD-L1 blockade therapy in various cancers. Furthermore, CCS1477 treatment resulted in a marked reduction of myeloid-derived suppressor cells (MDSCs) in the tumor microenvironment (TME) by inhibiting key cytokines such as IL6, CSF1, and CSF2, which are crucial for MDSC differentiation and recruitment. By reducing PD-L1 expression and modulating the immunosuppressive TME, CCS1477 creates a more favorable environment for tumor-infiltrating lymphocytes, significantly enhancing the efficacy of immune checkpoint blockade (ICB) therapy. Notably, these effects were observed in both prostate cancer and melanoma models, underscoring the broad therapeutic potential of p300/CBP bromodomain inhibition in improving ICB outcomes.

overall_design: RNA sequencing (RNA-seq) was performed on the prostate cancer cell line DU145, treated with either DMSO (control) or 1 μM CCS1477 for 24 hours to assess transcriptional changes induced by CCS1477 treatment.

first: Daheng

last: He


title: In situ detection and amplification of protein-protein interactions can increase recombinant protein production

city: La Jolla

first: Nathan

middle: E.

last: Lewis

state: CA

address: 9500 Gilman Dr. IBRFII, 5220E

department: Bioengineering; Pediatrics

institute: University of California, San Diego

summary: Recombinant proteins, in particular monoclonal antibodies and related molecules, have become dominant therapeutics. As they are produced in mammalian cells, they require the concerted function of hundreds of host cell proteins in the protein secretion pathway. However, the comprehensive set of host cell machinery involved remains unclear. Thus, it is often unknown why some recombinant proteins fail to express well. Here we present and deploy an approach called Fc-targeting Biotinylation by Antibody Recognition (FcBAR), which allows for the in situ detection of protein-protein interactions for any recombinant protein with Fc domain. Briefly, cells are permeabilized and incubated with an anti-Fc antibody, conjugated with horseradish peroxidase. All proteins interacting with Fc-bearing proteins are then biotinylated, pulled down and identified via mass spectrometry. We applied this method on a panel of rituximab-producing CHO-S clones with a range of productivity levels. Through analysis of FcBAR protein-protein interactions and RNA-Seq,  we identified protein interactions positively correlated with rituximab secretion, and tested 7 of these targets. We found overexpression of AGPAT4, EPHX1, and NSDHL significantly increased rituximab production. Thus, FcBAR provides an unbiased approach to measure PPIs supporting recombinant antibody production in situ, and can guide efforts to boost production of biotherapeutics and biosimilars by addressing production bottlenecks.

overall_design: RNA-seq profiling of the rituximab clones that produce at different levels of productivity.

first: Mina Ying Min

last: Wu

first: Frances

last: Rocamora

first: Mojtaba

last: Samoudi

first: Caressa M.

last: Robinson

first: Chih-Chung

last: Kuo

first: Nusa

last: Pristovsek

first: Henning Gram

last: Hansen

first: Lise Marie

last: Grav

first: Helene Faustrup

last: Kildegaard

first: Gyun Min

first: Alexandre Rosa

last: Campos

first: Nathan E.


title: NSUN2 Facilitates Dicer Cleavage of DNA Damage-Associated R-Loops to Promote Repair [ChIP-Seq]

city: Oxford

first: Monika

last: Gullerova

address: S Parks Rd

department: Sir William Dunn School of Pathology

institute: University of Oxford

summary: DNA integrity is constantly challenged by both endogenous and exogenous damaging agents, resulting in various forms of damage. Failure to repair DNA accurately leads to genomic instability, a hallmark of cancer. Distinct pathways exist to repair different types of DNA damage. Double-strand breaks (DSBs) represent particularly severe form of damage, due to physical separation of DNA strands. Repair of DSBs requires activity of RNA Polymerase II (RNAPII) and generation of Damage-associated transcripts (DARTs). Here we show that the RNA m5C-methyltransferase NSUN2 localizes to DSBs in transcription-dependent manner, where it binds to and methylates DARTs. Depletion of NSUN2 results in an accumulation of nascent DARTs around DSBs, specifically of the de novo primary DARTs. Furthermore, we detected an RNA-dependent interaction between NSUN2 and DICER, which was stimulated by DNA damage. NSUN2 activity promoted Dicer cleavage of DARTs associated R-loops, which is required for efficient DNA repair. We report a previously unrecognized role of the RNA m5C-methyltransferase NSUN2 within RNA-dependent DNA damage response, highlighting its function as a DICER chaperone for the clearance of non-canonical substrates such as DARTs, thereby contributing to genomic integrity.

overall_design: To investigate the role of NSUN2 in regulating processing of damage associated transcripts at genome-wide level, we emplyed NSUN2 5-Aza ChIP to detect the NSUN2 bound to m5C residues on chromatin bound RNA around DSBs in both mock and damage induced cells.

first: Adele

last: Alagia

first: Kamal

last: Ajit

first: Arianna

last: di Fazio


title: Cross-lineage m5C methylome profiling reveals methylated divergence in Toxoplasma tachyzoites

city: Taigu

first: Xiao-Nan

last: Zheng

address: No.1 Mingxian South Road

institute: Shanxi Agricultural University

summary: Toxoplasma gondii is a globally prevalent zoonotic parasite that chronically infects nearly one-third of the human population. Among emerging layers of gene regulation, 5-methylcytosine (m5C) has been recognized as a key post-transcriptional modification that modulates mRNA stability and translation in eukaryotes. However, the epitranscriptomic landscape of m5C in the tachyzoite stage of T. gondii remains uncharacterized. This study presents the first comprehensive profiling of m5C methylation across three major T. gondii genotypes—RH (type I), ME49 (type II), and VEG (type III)—using methylated RNA immunoprecipitation sequencing (MeRIP-seq) combined with RNA-Seq. Differentially m5C-methylated genes (DMMGs) were functionally annotated via Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses. Integration of methylation and transcriptomic data revealed strain-specific correlations between m5C modification and gene expression. Candidate m5C regulatory factors were identified through BLASTP searches in the ToxoDB database and further examined for expression and methylation patterns. We identified 5,129, 4,968, and 4,577 m5C-methylated genes in RH, ME49, and VEG tachyzoites, respectively, with methylation predominantly enriched within coding sequences (CDS). Comparative analysis revealed 1,710, 1,131, and 784 DMMGs across RH vs. ME49, RH vs. VEG, and ME49 vs. VEG comparisons. Functional enrichment highlighted DMMGs involved in catalytic activity, transport, phospholipid metabolism and transcription regulation. KEGG pathway analysis identified nucleocytoplasmic transport, DNA replication, and ATP-dependent chromatin remodeling as key m5C-regulated processes. Additionally, several putative m5C regulators were identified, displaying genotype-specific or conserved expression and methylation patterns, suggesting their potential roles in strain-specific phenotypic variation and as targets for therapeutic intervention. This study presents the first m5C epitranscriptomic atlas of T. gondii tachyzoites, revealing both conserved and genotype-specific mRNA modification networks. These findings offer critical insights into the regulatory role of m5C in T. gondii pathogenesis and open new avenues for the development of vaccines and therapeutics against zoonotic toxoplasmosis.

overall_design: MeRIP-seq and RNA-seq of  tachyzoites from three major T. gondii genotypes—RH (type I), ME49 (type II), and VEG (type III).

first: Hong-Yu

last: Song

first: Hany M.

last: Elsheikh

first: Qing

last: Liu

first: Wen-Bin

first: Xing-Quan

last: Zhu


title: Macrophage signaling and function are regulated by distinct sterol biochemistries

city: Sioux Falls

first: Kevin

last: Francis

state: SD

department: Cellular Therapies

institute: Sanford Research

summary: Membranes require continuous reorganization of lipid components, including sterols, to dynamically alter their rigidity to deform and bend during scission events which occur during fundamental cellular functions such as endocytosis.  While diseases of cholesterol biosynthesis result in reduced cellular cholesterol and accumulation of precursor sterols, limited studies have addressed the intracellular consequences of disease-associated sterol changes on the ability of eukaryotic cellular membranes to function and signal normally.  Here, we utilized bone marrow-derived macrophages (BMDMs) to investigate how altered sterol content impacts macrophage signaling and membrane function.  Through pharmacological inhibition of cholesterol biosynthetic enzymes, reduced cholesterol and increased levels of disease-associated sterol intermediates coincided with reduced expression of immunogenic surface markers and impaired macropinocytosis.  Macropinocytic activity was sensitive to both reduced plasma membrane cholesterol and sterols containing functional groups substituted for the C3 hydroxyl group.  Transcriptomic analyses of cholesterol-inhibited BMDMs revealed alterations in immune and chemokine signaling pathways.  Decreased cholesterol was also associated with dysregulated vesicular sorting pathways and elevated expression of endosomal/lysosomal markers.  Disrupted endosomal sorting and impaired macropinocytosis was also observed in BMDMs from mouse models of the cholesterol biosynthesis disorder Smith-Lemli-Opitz syndrome (SLOS).  Our findings detail an important connection between sterol imbalance, membrane dynamics, and immune cell function.

overall_design: RNAseq profiling of bone marrow derived macrophage cultured in fetal bovine serum, lipoprotein deficient fetal bovine serum (LPDS) for 48 h, LPDS +Dhcr7 inhibitor AY9944, LPDS + HMG-CoA reductase inhibitor simvastatin, or LPDS + Dhcr24 inhibitor U18666A

first: Jazmine

middle: D

last: Yaeger

first: Jason

middle: G

last: Kerkvliet

first: Bijaya

last: Pradhan

first: Amelia

last: Lawver

first: Sonali

last: Sengupta

first: Natalie

last: Thiex


title: Testing the contribution of FGL1 to the pathogenesis of metabolic dysfunction-associated steatotic liver disease and hepatocellular carcinoma

city: Toulouse

first: Jean

last: Personnaz

address: CHU Purpan pavillon Lefebvre, av des arènes romaines

department: IRSD

country: France

institute: Inserm

summary: Metabolic dysfunction-associated steatotic liver disease (MASLD) begins with simple steatosis, which can progress to hepatocellular carcinoma (HCC). The pathogenesis of MASLD alters the secretion of hepatokines such as fibrinogen-like 1 (FGL1), a candidate mediator of liver steatosis and hyperglycemia. To investigate the contribution of FGL1 to liver diseases, we compared wild-type mice to mice with hepatocyte-specific deletion of Fgl1 subjected to a steatosis or HCC experimental protocol. We found that mice deficient for Fgl1 in hepatocytes showed higher levels of plasma glucose, pronounced metabolic alterations and liver injury when fed a western diet compared to their wild-type counterparts. However, both genotypes exhibited a similar lipid deposition in the liver. Similarly, wild type and Fgl1-deficient mice displayed comparable liver alterations during HCC progression. We observed that FGL1 expression was repressed during MASLD progression in mice and human concomitantly with the severity of liver injury. Altogether, these findings suggest that FGL1 is not a major contributor to the pathogenesis of MASLD and HCC.

overall_design: Liver bulk RNA-seq profiling from 8 weeks-old Fgl1WT and Fgl1LKO male mice,

first: Leon

last: Kautz


title: Effect of encapsulating peritoneal sclerosis modeling on mice peritoneums

city: Houston

first: Yuxiang

last: Sun

state: Texas

address: One Baylor Plaza, Houston, TX, 77030, United States

institute: Baylor College of Medicine

summary: Encapsulating peritoneal sclerosis (EPS) is a life-threatening fibrotic condition characterized by severe abdominal adhesions, chronic inflammation, and significant morbidity. The lack of effective treatments for EPS stems from a limited understanding of its underlying mechanisms. Previous EPS models relied on intraperitoneal injection of surgical hygiene solution (SHS), requiring 8 weeks to establish. Here, we modified the model by integrating both PD and lipopolysaccharide (LPS), leading to the formation of stable adhesions in just 3 weeks.This model better simulates the pathophysiological progression of EPS by reflecting more clinically relevant risk factors, such as PD and peritonitis, and captures key features like inflammatory infiltration and extracellular matrix (ECM) deposition.

overall_design: C57BL/6J male mice, aged 8 weeks,were received daily intraperitoneal injections of 100 mL/kg of 4.25% peritoneal dialysis solution (PDS) and 0.3 mL SHS, along with a single weekly intraperitoneal injection of 4 mg/kg lipopolysaccharide (LPS). And mice received the same volume of saline were used as controls. Mice were sacrificed in the 3rd week, when significant intra-abdominal adhesion formation was observed in the EPS modeling mice.

first: Peng

last: Hui

first: Hu

last: Zhaoyong


title: RNA-Seq experiments for  isolated mice tissues in both WT and Mut mice

city: Bethesda

first: Haiming

last: Cao

state: MD

address: 9000 Rockville Pike

department: NHLBI

institute: NIH

summary: The  male mice were housed in groups of three per cage, with unrestricted access to water and a standard chow diet.

overall_design: Heart, muscle, liver, and brown adipose tissue (BAT) were isolated from wild-type (WT) and Mut (SMIM30 knockout) mice. These tissues were immediately preserved in liquid nitrogen post-sacrifice to maintain their integrity for subsequent analyses.. Each tissue was collected from four individual male mice.

first: Yonghe

last: Ma


title: A phosphorylation switch within the Mediator subunit MED15 controls cellular senescence and cognitive decline

city: Shanghai

first: Yuanming

last: Zheng

address: 220 Handan Rd., Shanghai

institute: fudan university

summary: A hallmark of aging is chronic systemic inflammation, which is exacerbated by the hypersecretory aging phenotype known as the senescence-associated secretory phenotype (SASP). How the SASP is initiated to accelerate tissue inflammation and aging is an outstanding question in ageing biology. Here, we showed that phosphorylation of the mediator subunit MED15 at T603 is able to control the SASP and aging. Transforming growth factor-β (TGFβ) selectively induces CDK1-mediated MED15 T603 phosphorylation to control SASP gene expression. The MED15 T603 dephosphorylated mutant (T603A) inhibits the SASP and cell senescence, whereas the T603 phosphorylation-mimicking mutant (T603D) has the opposite effect. Mechanistically, forkhead box protein A1 (FOXA1) preferentially binds to unphosphorylated but not phosphorylated MED15 at T603 to suppress SASP gene expression. Notably, aging mice harboring dephosphorylated mutation in this phosphosite exhibit improved learning and memory through the attenuation of the SASP across tissues. Overall, our study indicates that MED15 T603 phosphorylation serves as a control switch for SASP production, which underlies tissue aging and cognitive decline and provides a novel target for age-related pathology.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: To investigate the function of MED15 T603 phosphorylation, we generated MED15 T603A HaCaT cell line and T603D MCF7 cell line and performed RNA-seq analysis. The WT and  MED15 T603A HaCaT were treated with or with TGFβ for 3 hours. We further performed RNA-seq analysis of hippocampus in aging WT and Med15 T604A mice (17-20M).

first: Haozheng

last: Li

first: Gang

last: Wang