Abstract 5719: Contrasting roles of MSH2 and MLH1 in basal-like breast cancer

Cancer Research · 2026-04-03

Abstract Basal-like breast cancer (BLBC) is the most aggressive molecular subtype of breast cancer, characterized by high genomic instability. Because of higher mutational load and genetic heterogeneity in BLBC, cancer cells tend to upregulate DNA repair pathways. Therefore, DNA repair-based therapies are considered to have significant potential for BLBC patients. PARP (Poly (ADP-ribose) polymerase) inhibitors are approved by FDA to treat a subset of BLBC patients with BRCA1/2 mutations. However, most BLBC patients have wildtype BRCA1/2 and lack good therapeutic targets. We analyzed all available DNA repair genes and proteins using TCGA RNA-sequencing and RPPA (Reverse Protein Phase Array) data. Our investigation identified that mismatch repair (MMR) proteins MSH2 and MSH6 (referred to as MutSα) are highly elevated in BLBC and their higher expressions are correlated to poor survivals of BLBC patients. Conversely, MLH1 and PMS2 (referred to as MutLα), the second major component of the MMR machinery, are downregulated at the mRNA level and cannot predict patient survival in BLBC. In contrast to the known tumor suppressor functions of MMR proteins, our data indicates that MSH2 promotes BLBC metastasis; MLH1, on the other hand, is associated with decreased tumor progression and metastasis. The contrasting functions of MSH2 and MLH1 have never been reported. At the mechanistic level, our data strongly indicate that MSH2, in contrast to MLH1, regulates the expression of chemokines and tumor infiltrating immune cells. Further investigation at the genomic level suggests that MSH2 regulates the expression of interferon alpha/beta receptor 1 (IFNAR1), which plays various roles in the tumor microenvironment (TME) for potential antitumor effects. Deletion of MSH2 initiates a chain of immune reactions via the upregulation of IFNAR1 expression which explains a highly immune active TME in tumors with MSH2-deficiency. Our study supports the contrasting functions of MSH2 and MLH1 in BLBC progression are due to their distinct transcriptional regulation of immune related genes, not related to their canonical mismatch repair activity. These findings challenge the universal paradigm that all MMR proteins have similar effects on tumor progression or suppression. Citation Format: Tanzia Islam Tithi, Jiao Mo, Nicholas Borcherding, Sung Jo, Heather R Kates, Chandra Maharjan, Seyedehalaleh Anvar, Richard L. Bennett, Jixiu Shan, Rohan A. Desai, Kailey E Cash, Masayoshi Honda, Lei Wang, Kawther K. Ahmed, Kalyanee Shirlekar, Li Chen, Katherine N. Gibson-Corley, Ronald Weigel, Jonathan D. Licht, Maria Spies, Ryan Kolb, Weizhou Zhang. Contrasting roles of MSH2 and MLH1 in basal-like breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 5719.

Mass Spectrometry-Based Spatial Imaging of the Cochlea

Journal of the American Society for Mass Spectrometry · 2026-04-03

Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Imaging (MALDI-MSI) is transforming spatial molecular studies. However, applying MALDI-MSI to small, anatomically complex tissues remains challenging. One such structure is the cochlea, the auditory part of the inner ear that is critical for hearing. To address these challenges, we developed and implemented a streamlined workflow for sample preparation and processing to obtain MALDI-MSI data on mouse cochlea. Sample acquisition was optimized to minimize time and processing steps, allowing use of flash-frozen neonatal mouse heads. This workflow enabled high spatial resolution metabolomic and lipidomic imaging of the sagittally cryosectioned mouse cochlea using N-(1-naphthyl) ethylenediamine dihydrochloride (NEDC) matrix via sublimation. Optimized NEDC sublimation allowed high signal-to-noise, reduced delocalization, and salt tolerance, allowing acquisition of 5 μm-resolution imaging data on a MALDI-MSI instrument. Sublimation was found to be superior to spraying as a method for matrix application due to its higher signal-to-noise, particularly for lipids and fatty acids, and improved spatial resolution. Diverse metabolites and lipids were measured throughout the cochlear region, revealing distinct spatial distributions. Clustering identified reproducible physiological regions, including the otic capsule and spiral ducts. High spatial resolution imaging revealed distinct tissues, cell types, and molecular signatures within the cochlea. These findings establish the utility of high spatial resolution MALDI-MSI for auditory research, enabling molecular mapping of cochlear function and dysfunction.

Multi-omics analyses reveal the regulatory mechanisms of 25-hydroxycholecalciferol to improve meat quality in Pekin ducks

Journal of Agriculture and Food Research · 2025-11-26

This study investigated the effects of dietary supplementation with vitamin D 3 (VD 3 ) or 25-hydroxycholecalciferol (25-OH-D 3 ) on the Pekin ducks meat quality using multi-omics (lipidomics, metabolomics, and transcriptomics). Male Pekin ducks (15-d-old, N = 168) were allocated to 3 groups, with 8 replicates of 7 ducks from 15 to 42 d. Experimental diets included the control diet lacking vitamin D, a diet with 1,200 IU/kg VD 3 or 1,200 IU/kg 25-OH-D 3 . Both VD 3 and 25-OH-D 3 increased carcass weight, carcass rate, eviscerated weight, and breast meat weight of Pekin ducks. VD 3 or 25-OH-D 3 supplementation enhanced plasma 25-OH-D 3 concentrations, breast meat redness, total antioxidant capacity, and total superoxide dismutase activity in plasma and breast meat, while 25-OH-D 3 exhibited more pronounced effects than VD 3 . Compared to the Control and VD 3 group, 25-OH-D 3 increased breast meat pH 45min and pH 24h , and decreased yellowness. Compared to the VD 3 group, 25-OH-D 3 enhanced breast meat polyunsaturated fatty acid (PUFA), n-6 PUFA, and n-3 PUFA contents. Lipidomics and metabolomics revealed that 25-OH-D 3 increased breast meat diacylglycerol (ether bond), taurine-derived, and L-arginine, etc. Compared to the Control and VD 3 group. Transcriptomics revealed that 25-OH-D 3 upregulated ApoA4 , ApoC3 , ApoH , and HMGCS2 compared to the Control and VD 3 group, which may promote the synthesis of taurine derivatives and thus enhance antioxidant capacity. In conclusion, supplemental vitamin D improves breast meat quality of Pekin ducks, while 25-OH-D 3 is more effective in potentiating antioxidant status, activating lipid transport. • VD 3 or 25-OH-D 3 supplementation increased breast meat weight of Pekin ducks. • 25-OH-D 3 exceeded VD 3 in improving meat color and pH, both raised T-SOD and T-AOC. • 25-OH-D 3 upregulated breast taurine derivatives, APOA4 , APOC3 , APOH , and HMGCS2. • 25-OH-D 3 improved meat quality by enhancing antioxidant and lipid transport.

Prospective study of patient-reported depression, and cognitive and functional impairment, and impact on survival and induction mortality in fit adults age ≥60 years receiving intensive chemotherapy (IC) for Acute Myeloid Leukemia (AML): Prospective geriatric assessment (GA) report from ECOG-ACRIN (EA) E2906 randomized study

Blood · 2025-11-03

Abstract Background We performed a prospective study evaluating a baseline GA battery and clinical outcomes in fit older adults (age ≥60 years) with AML and normal cardiac and renal function in the recent E-A NCTN E2906 phase 3 study. A patient-reported outcomes (PRO) assessment of Depression, Activities of Daily Living (ADL), Cognitive Function, Social Support (SS) domains, and comorbidity was performed at study registration to evaluate the prevalence of vulnerabilities and their impact on overall survival (OS) and 30-day induction mortality rates (IM) in this cohort selected for fitness to receive IC. Methods E2906 study design and results have been presented previously [n=727, age ≥60 years, randomized 1:1 to ‘standard 7&3‘ & high dose cytarabine (Arm A) vs. single agent clofarabine (CLO, Arm B), as remission induction (Step 1) and consolidation (Step 2)]. There was no difference in composite complete remission (CCR, 50%) or IM (8.5%), and CLO was inferior for OS. A baseline GA was a key secondary protocol objective, offered to all patients, and n=532 (73%) participated. We assessed Geriatric Depression Scale (GDS, none vs. any depressive symptoms, n=524); cognitive screen using Mini-Mental Exam Section (MMES, score 8/8 vs. <8, n=516); ADL & Instrumental ADL (iADL), (need for assistances vs. not n=526); a Medical Outcomes Study SS Survey (MOS-SS, measured as per unit increase, n=527); a Comorbidity survey ( ≤4 vs. ≥5 patient-reported comorbidities, n=530), patient-reported prescription medications use (PM, 0-3 vs. ≥4, n=519); and a survey of Sexual Desire (n=491) and Sexual Activity (n=477) within 4 weeks of AML diagnosis. Association of GA domains with OS, IM, and achievement of CCR was evaluated using the Chi-squared, Fisher's exact, and Wilcoxon rank sum test. Survival analysis was performed using the Cox proportional hazards models, adjusted for treatment arm. All p-values are 2-sided. Results The median age among those participating in GA battery was 67 yrs (range 60-85), including 38% age ≥70. There were 42% females, and ECOG performance status was 0 (28%), 1 (54%), 2 (16%), or 3 (2%). Central Cytogenetic review was classified (ELN2017) as Favorable (3%), Intermediate (66%), and Adverse (31%) risk. There was a notable rate of GA scores outside ‘normal’ clinical cutoff, including Depression (GDS 31%), cognitive and functional impairment [MMSE (37%), ADL (25%) and iADL (32%)], ≥5 Comorbidities (23%), and ≥4 PM's (44%). 81% & 76%, respectively, reported no sexual activity and low/none sexual desire. MOS-SS tended to be high in this cohort [mean (SD) score 87 (17)]. We observed a significant association of GA domains with OS & IM. For OS, absence of depressive symptoms [GDS, Hazard Ratio (HR) 0.79, 95% confidence Intervals (CI) 0.64-0.97, p=0.025)], MMES 8/8 (HR 0.78, 95%CI 0.64-0.96, p=0.016), requiring no assistance with ADLs (HR 0.65, 95%CI 0.52-0.82, p<0.001) and iADLs (HR 0.69, 95%CI 0.57-0.85, p<0.001), and ≤4 Comorbidities (HR 0.68, 95%CI 0.54-0.84, p=0.001) were significant for superior OS; use of ≥4 PM's was associated with inferior OS (HR 1.32, 95%CI 1.09-1.61, p=0.005). There was no association of sexual activity/desire, BMI ≥30 kg/m2, or MOS-SS with OS. IM was significantly higher among those with any depression symptoms (GDS, p=0.005), any ADL (p=0.010) or iADL (p=0.013) impairment, ≥5 comorbidities (p=0.037) and ≥4 PM's (p=0.001); there was no association with MOS-SS or MMES. There was no significant association of GA scores with cytogenetic risk group or with CCR rates. Only ADL independence (p=0.048), and possibly Comorbidity ≤4 (p=0.071), were associated with proceeding to Step 2. Conclusions In this large prospective cohort of fit older adults with AML selected to receive IC, we observed high rates of PRO-assessed GA vulnerability, which was significantly associated with inferior OS and higher IM rates, and (for ADL impairment) lower rates of proceeding to consolidation therapy. This suggests that functional and cognitive impairments are prevalent and can significantly impact outcome even in fit older adults. Despite potential long-term OS advantages of IC previously observed in E2906, efforts to systematically recognize those at higher risk based on GA PROs are needed to help identify patients who may be more appropriate for study of lower intensity treatment options to mitigate impact on IM and OS. SImilarly we plan to evaluate the potential benefit of GA-driven supportive care to improve patients' outcomes.

Coronavirus M protein impairs cilium during early infection by enhancing the AurA-HDAC6 axis

PLoS Pathogens · 2025-09-12 · 1 citations

Coronaviruses (CoVs) are implicated in human outbreaks and significant economic losses in the porcine and avian industries. Recent investigations have underscored the potential role of cilia within the respiratory tracts of infected hosts, particularly regarding the entry of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, the mechanisms by which other CoVs exert their virulence through ciliary interactions remain inadequately elucidated. In this context, our research has demonstrated that porcine epidemic diarrhea virus (PEDV) and porcine deltacoronavirus (PDCoV) induce ciliary disassembly within six hours post-infection during the early infection stage. Utilizing mass spectrometry, we identified histone deacetylases 6 (HDAC6) or Aurora A (AurA) as binding partners of PEDV or PDCoV membrane (M) proteins. Immunofluorescence studies corroborated that the AurA-HDAC6 axis serves as a principal regulator of ciliary disassembly. Additionally, M proteins from all four CoV genera-PEDV, SARS-CoV-2, PDCoV, and infectious bronchitis virus (IBV)-were observed to congregate at the ciliary base. Molecular techniques, including immunoprecipitation and molecular docking combined with molecular mechanics/generalized born surface area (MM/GBSA) free energy decomposition analysis, further revealed that CoV M proteins interact with both AurA and HDAC6. These interactions depend on conserved residues at the transmembrane-cytosolic junction of M proteins, essential for their binding to the AurA-HDAC6 axis. Mutations disrupting these residues significantly impaired the binding affinity, thus inhibiting the associated ciliary disassembly process. Collectively, our findings illuminate a conserved regulatory mechanism involving CoV M proteins across all four genera, contributing to ciliary disassembly during early infection. This work enhances our understanding of the fundamental interactions between CoVs and host cells, positioning AurA and HDAC6 as potential therapeutic targets for a broad spectrum of CoV infections.

A myeloid Tet2-IL-1β axis modulates intestinal inflammation by restricting catecholaminergic stimulation of enterochromaffin cell differentiation

Immunity · 2025-11-01 · 2 citations

CpG-oligodeoxynucleotides challenged macrophages ameliorate acetaminophen induced liver injury by activating TLR9/IRG1/itaconate metabolic pathway

Molecular Medicine · 2025-08-25 · 3 citations

BACKGROUND: Acetaminophen, or N-acetyl-para-aminophenol (APAP), causes severe liver damage and acute liver failure when overdosed. Oligodeoxynucleotides containing CpG motifs (CpG ODN) can regulate the function of macrophages, which play an important role in drug-induced liver injury. It is unclear whether CpG ODN-treated macrophages play an immune regulation role in APAP-induced liver injury. In the present study, we aim to explore the role of CpG ODN-activated macrophages in APAP-induced liver injury and the underlying mechanism in protecting against the cytotoxicity of APAP. METHODS: In vivo, C57BL/6 mice were treated with APAP (300 mg/Kg) or/and CpG ODN (ODN 1826, 1.65 mg/Kg) by intraperitoneal injection, then survival rate, histopathological evaluation, and inflammatory factors were observed to ascertain the protective effect of CpG ODN. Then, CpG ODN-treated macrophages were reinfused into the animal model to determine the effector cells. In vitro, RNA sequencing and untargeted metabolomics detection were performed to illustrate the underlying mechanism. Last, Acod1 siRNA interference was used to clarify the role of IRG1 in resistance to APAP cytotoxicity by ROS and apoptosis indicator detections. RESULTS: We found that CpG ODN showed a protective effect against APAP cytotoxicity by stimulating macrophages rather than hepatic parenchymal cells. In particular, reinfusion of CpG ODN-treated macrophages to mice can alleviate APAP-induced liver injury. Transcriptome and metabolome analysis revealed that the expression of aconitate decarboxylase 1 (Acod1; also known as immune responsive gene 1, IRG1) and the metabolite itaconate generated by IRG1 catalysis increased after CpG ODN stimulation. In addition, we found that the mechanism of this protective effect is ascribed to the increased expression of Acod1 and the antioxidative function of itaconate by the activation of the TLR9/NF-κB signaling pathway. CONCLUSION: CpG ODN alleviated liver injury induced by APAP through the activation of the TLR9/NF-κB signaling pathway in macrophages, upregulating the expression of IRG1 protein, promoting the production of endogenous metabolite itaconate, and inhibiting macrophage apoptosis which was regulated by upregulating the expression of Nrf2 to inhibit ROS production. This study sheds new light on CpG ODN as a therapeutic strategy in resistance to APAP-induced liver injury.

Polymerase Ѳ inhibitors combinations with approved and investigational agents in patient-derived tumor multi-cell type (mct) spheroids

Experimental and Molecular Pathology · 2025-06-27 · 2 citations

The potential of novobiocin, recently identified to be a DNA POLѲ inhibitor, to augment cancer chemotherapy was explored in the late 1980s and early 1990s in tumor cells, tumor-bearing mice and in Phase 1 clinical trial in combination with cyclophosphamide or cisplatin. Genetic alterations which may increase or decrease POLѲ inhibitor effects have been elucidated. Thirty patient-derived tumor cell lines with known BRCA, ATM, ATR, POLѲ, XRCC1, PALB2, PARP1, LIG3 alterations as well as know gLOH% and MSI status were screened in a mct-spheroid assay (tumor cells, endothelial cells, mesenchymal stem cells) with a POLѲ inhibitor, novobiocin, ART-558, and RP6685, alone or in simultaneous combination with a FDA-approved or investigational anticancer small molecule with a 7-day exposure and a CellTiter-Glo 3D luminescence endpoint. As single agents, the POLѲ inhibitors had little or no cytotoxicity. In simultaneous combination with ART-558, talazoparib produced greater-than-additive cytotoxicity at the highest concentrations of the POLѲ inhibitors in the 922,993-354-T-J3-PDC endometrial serous carcinoma mct-spheroids. Activity of the Chk1/2 inhibitor prexasertib was potentiated by either ART-558 or RP6685 in the 922,993-354-T-J3 mct-spheroids. The combination of POLѲ inhibitors ART-558 and RP6685, and the Chk1/2 inhibitor prexasertib produced up to 1 log increase in cytotoxicity in the 922,993-354-T-J3 mct-spheroids. Regions of potentiation were evident in the 922,993-354-T-J3-PDC endometrial carcinoma survival surface plots at the highest concentration of paclitaxel tested, while regions of potentiation were evident in the paclitaxel mid-concentrations of the 299,254-011-R-J1-PDC melanoma mct-spheroids survival surface plots as determined by the Bliss independence calculation. DNA POLѲ is recruited to DNA double-strand breaks as a component of repair. POLѲ allosteric inhibitors, novobiocin, ART558 and RP-6685, have entered clinical trial. The current study explores the cytotoxicity of POLѲ inhibitors in combination with anticancer drugs and investigational agents in patient-derived cell lines grown as mct-spheroids.

BayesCNet: Bayesian inference for cell type-specific regulatory networks leveraging cell type hierarchy in single-cell data

bioRxiv (Cold Spring Harbor Laboratory) · 2025-09-17

Understanding gene regulatory networks (GRNs) is essential for deciphering biological processes and disease mechanisms. Single-cell multiome technologies now enable joint profiling of chromatin accessibility and gene expression, offering an powerful means to infer cell type-specific GRNs. However, existing methods analyze each cell type independently or aggregate data into pseudo-bulk profiles, limiting their ability to resolve rare populations and capture cellular heterogeneity. We introduce BayesCNet, a Bayesian hierarchical model that jointly infers enhancer-gene linkages across all cell types while leveraging their hierarchical relationships for information sharing. Through extensive simulations, BayesCNet consistently outperforms state-of-the-art methods, with the largest improvements in rare cell types. When applied to real datasets, BayesCNet identifies enhancer-gene linkages with higher accuracy validated by promoter-capture Hi-C data, and reconstructs cell type-specific GRNs that highlight key regulators, demonstrating its power to resolve gene regulatory programs across diverse cell types.

Physiological and Transcriptomic Insights Into the Regulatory Effects of Methyl Jasmonate on Growth and Bioactive Compounds of <scp> <i>Dendrobium nobile</i> </scp>

Physiologia Plantarum · 2025-11-01

ABSTRACT Methyl jasmonate (MeJA) is a key plant growth regulator that influences growth and medicinal compound accumulation in Dendrobium nobile . This study investigated the effects of different MeJA concentrations (0, 100, 200, 400, and 800 μmol l −1 ) and identified 200 μmol l −1 as the optimal concentration for significantly enhancing growth, physiological traits, and bioactive compound synthesis after a 28‐day treatment. The 200 μmol l −1 MeJA treatment markedly improved plant height, stem diameter, leaf size, and photosynthetic pigment content. It also boosted antioxidant enzyme activities while reducing malondialdehyde levels and increasing osmolyte content. Furthermore, this treatment significantly elevated the accumulation of polysaccharides, total flavonoids, and polyphenols. MeJA treatment was associated with altered expression of MYC2 and JAZ, suggesting possible activation of JA signaling, concurrently promoting the expression of key genes involved in flavonoid and polyphenol biosynthesis, such as CHS , CHI , and 4CL . qRT‐PCR validation of 12 differentially expressed genes (DEGs) showed strong concordance with the transcriptomic data. The validated DEGs included key genes involved in phenylpropanoid/flavonoid biosynthesis ( CYP73A , HCT , COMT , UBC , and CHI ), plant hormone signal transduction ( JAZ , PYL , PP2C , and GH3 ) and plant‐pathogen interaction ( CALM , RIN4 , and CPK ). These results suggest that 200 μmol l −1 MeJA may enhance both the medicinal quality and stress adaptation of D. nobile , providing insights for the targeted application of phytohormones in its cultivation.