Biology subjects

Nandu, T.

Publications and source records attributed to Nandu, T..

10 recordsLinked to original sources

bioRxiv2025

Mapping the Subtype-Specific PARP1 ADP-ribosylated Proteome in Breast Cancer Cells

Breast cancers are molecularly heterogeneous, with subtype-specific differences in transcriptional programs, chromatin architecture, and therapeutic responses. While PARP1 has been extensively studied in the context of DNA repair, emerging evidence implicates its catalytic activity in a broader set of cellular processes, including the regulation of gene expression. Here, we employed an NAD analog-sensitive PARP1 (asPARP1) chemical genetics approach combined with mass spectrometry to map the ADP-ribosylated proteome across six human breast cancer cell lines representing luminal and basal/triple negative subtypes. We identified thousands of PARP1 substrates and hundreds of Glu/Asp ADPRylation sites, revealing both shared and subtype-specific modifications in cell lines maintained under basal growth conditions. Luminal-specific substrates were enriched in chromatin and transcriptional regulators, whereas basal-specific substrates were preferentially linked to translation and RNA processing, highlighting lineage-dependent PARP1 activity. Transcription factors emerged as major substrates, with TFAP2A serving as a proof-of-concept; it is selectively ADPRylated in luminal cells and inhibition of PARP1-mediated ADPRylation modulates its promoter occupancy in a subtype-specific manner. Our data provide a new resource for studying subtype-specific PARP1-mediated ADPRylation in breast cancer cells. Collectively, our findings expand the conceptual framework for PARP1 function beyond DNA repair, offering mechanistic insights into subtype-specific gene regulation and potential determinants of PARP inhibitor sensitivity in breast cancer.

cancer biology↗

bioRxiv2025

Estrogen Receptor Enhancers Sensitive to Low Doses of Hormone Specify Distinct Molecular and Biological Outcomes

Adult women are typically exposed to estradiol (E2) concentrations of [~]100-200 pM, yet most cell-based studies use 100 nM. We determined the molecular effects of E2 concentrations spanning six orders of magnitude (1 pM to 100 nM) in breast cancer cells. Estrogen receptor alpha (ER) enhancers formed at low physiological doses of E2 (1-100 pM) are mechanistically distinct from those that form at high pharmacological doses (10-100 nM). They (1) form in open chromatin bound by FOXA1, (2) produce enhancer RNAs enriched with functional eRNA regulatory motifs (FERMs), and (3) drive expression of cell proliferation genes with promoter-proximal paused RNA polymerase II. Importantly, low dose ER enhancer usage is elevated in breast cancer patients with poor responses to aromatase inhibitors, likely as a continued response to low circulating levels of E2. Collectively, our results identify mechanistic differences between low and high dose ER enhancers that specify distinct biological outcomes.

genomics↗

bioRxiv2025

Role of Macrophage PARP1 in the Regulation of Crosstalk between Adipose Immune Cells and Adipocytes during Diet-induced Obesity

Adipose tissue consists of heterogeneous cell populations, including macrophages, which play a key role in maintaining adipose tissue homeostasis. We previously identified PARP1 as a critical regulator of proadipogenic gene expression in preadipocytes and proinflammatory gene expression in macrophages. To investigate the role of macrophage PARP1 in regulating adipose tissue homeostasis, we generated myeloid lineage-specific Parp1 knockout mice (Parp1 KOLysM). When subjected to a high fat diet for 12 weeks, the Parp1 KOLysM mice exhibited an obese phenotype accompanied by white adipose tissue (WAT) dysfunction, characterized by altered metabolite profile, pronounced adipocyte hypertrophy, and increased macrophage infiltration. Coculture of primary preadipocytes with the conditioned medium from bone marrow-derived macrophages (BMDMs) isolated from Parp1 KOLysM or control mice demonstrated that macrophage PARP1 depletion inhibited LPS-induced proinflammatory gene expression in BMDMs, but enhanced differentiation of preadipocytes into mature adipocytes. Single cell RNA-sequencing using CD45+-sorted WAT resident immune cells showed that macrophage PARP1 depletion increased the fraction of macrophages and NK cells, altered gene expression in both cell populations, and promoted intercellular communications. Taken together, our studies demonstrate a key role for macrophage PARP1 in the maintenance of adipose tissue inflammatory and metabolic homeostasis. Macrophage PARP1 depletion promotes cell-cell crosstalk among macrophages, fat cells, and other immune cell populations in adipose tissue, which cooperatively drives the development of obesity. SignificanceIn this study, we characterized a role for macrophage PARP1 in regulating adipose tissue homeostasis. Depletion of PARP1 in macrophages enhances cell-cell crosstalk among immune cells and fat cells, which exacerbates adipose dysfunction and drives obesity and adverse metabolic outcomes.

molecular biology↗

bioRxiv2025

Phenotypic and Functional Characterization of Oncohistone Mutations in Breast Cancers

Although mutations in genes encoding histones display a similar prevalence to that of some other somatic mutations in cancer, the underlying mechanisms by which histone mutations drive tumorigenesis have not been fully explored. Herein, we curated missense mutations occurring in core histone genes in breast cancers using data from MSK-IMPACT and cBioPortal to identify high frequency breast cancer-associated histone gene mutations. We characterized 17 high frequency oncohistone mutations in H2A H2B, and H3 that are enriched in breast cancer samples and occurred at glutamate (E), aspartate (D), serine (S), and arginine (R) residues. Many of these mutants co-occur with PIK3CA mutations in breast cancer samples. The oncohistone mutants were expressed in MCF-7 breast cancer cells or MCF-10A mammary epithelial cells and screened for effects on oncogenic phenotypes in a variety of cell- and tumor-based assays (i.e., proliferation, migration, invasion, competitive outgrowth, transformation). In addition, we examined the effects of selected mutants on DNA damage and gene expression. Our results indicate that the collection of oncohistone mutants that we screened have varying phenotypic and functional effects. Some can promote cancer-related phenotypes, with H2B-E76Q, H3-E97K, and H3-E105K eliciting strong oncogenic phenotypes and alterations in gene expression. All three of these mutants showed cooperativity with an activating mutation in PIK3CA (E545K), or a chemical activator of PI3K (UCL-TRO-1938), in assays of MCF-10A proliferation. H3-E105K also strongly promoted transformation of MCF-10A cells in an assay of growth on low attachment substrate independently of PIK3CA. Our results indicate that some high frequency oncohistone mutants can have oncogenic activity in breast cancers, and may act as potential cancer drivers. Collectively, these observations presented here can be used as a resource to connect biological and molecular outcomes to oncohistones in breast cancers. SignificanceIn this study, we identified and characterized 17 high frequency oncohistone mutations in H2A H2B, and H3 that are enriched in breast cancer samples and promote cancer-related phenotypes when expressed in cells. Many of these oncohistone mutations co-occur in breast cancer samples with mutations in PIK3CA, the most frequently mutated gene in breast cancer, and may act as potential cancer drivers.

cancer biology↗

bioRxiv2025

NAD+ Sensing by PARP7 Regulates the C/EBPβ-Dependent Transcription Program in Adipose Tissue In Vivo

We have identified PARP7, an NAD+-dependent mono(ADP-ribosyl) transferase, as a key regulator of the C/EBP{beta}-dependent proadipogenic transcription program. Moreover, PARP7 is required for efficient adipogenesis and downstream biological functions, including involution of the lactating mammary gland. PARP7 serves as a coregulator of C/EBP{beta}, and depletion of PARP7 causes a dramatic reduction in C/EBP{beta} binding across the genome. PARP7 functions as a sensor of nuclear NAD+ levels to control gene expression. At the relatively high nuclear NAD+ concentrations in undifferentiated preadipocytes, PARP7 is catalytically active for auto- mono(ADP-ribosyl)ation (autoMARylation). As nuclear NAD+ concentrations decline post- differentiation, autoMARylation decreases dramatically. AutoMARylation promotes instability of PARP7 through an E3 ligase-ubiquitin-proteasome pathway mediated by the ADP-ribose (ADPR)-binding ubiquitin E3 ligases DTX2 and RNF114. Genetic depletion of PARP7 in mice promotes a dramatic reduction in a wide array of lipids in the mammary gland fat pads and milk from lactating females, as well as a significant decrease in nicotinamide mononucleotide (NMN), a key nutrient in mothers milk. The latter is due to reduced expression of Nampt, the gene encoding NAMPT, the enzyme that produces NMN, which is a direct transcriptional target of PARP7 and C/EBP{beta}. Collectively, our results extend the biology of PARP7 to adipogenesis and perinatal health. Moreover, our results describe the molecular events that regulate these downstream biological functions.

cell biology↗

bioRxiv2025

X-Linked Cancer-Associated Polypeptide (XCP) from lncRNA1456 Cooperates with PHF8 to Regulate Gene Expression and Cellular Pathways in Breast Cancer

Recent studies have demonstrated that a subset of long "noncoding" RNAs (lncRNAs) produce functional polypeptides and proteins. In this study, we discovered a 132 amino acid protein in human breast cancer cells named XCP (X-linked Cancer-associated Polypeptide), which is encoded by lncRNA1456 (a.k.a. RHOXF1P3), a transcript previously thought to be noncoding. lncRNA1456 is a pancreas- and testis-specific RNA whose gene is located on chromosome X. We found that the expression of lncRNA1456 and XCP are highly upregulated in the luminal A, luminal B, and HER2 molecular subtypes of breast cancer. XCP modulates both estrogen-dependent and estrogen-independent growth of breast cancer cells by regulating cancer pathways, as shown in cell and xenograft models. XCP shares some homology with homeodomain-containing proteins and interacts with the histone demethylase plant homeodomain finger protein 8 (PHF8), which is also encoded by an X-linked gene. Mechanistically, XCP stimulates the histone demethylase activity of PHF8 to regulate gene expression in breast cancer cells. These findings identify XCP as a coregulator of transcription and emphasize the need to interrogate the potential functional roles of open reading frames originating from noncoding RNAs. Statement of SignificangeXCP, a polypeptide encoded by an X-linked lncRNA, regulates gene expression in breast cancer cells. XCP is a chromatin-associated protein that interacts with the histone demethylase PHF8 and modulates its demethylase activity to regulate gene expression. XCP drives cancer-specific phenotypes and serves as a potential biomarker and/or target for therapeutic intervention.

cancer biology↗

bioRxiv2024

KAP1 negatively regulates RNA polymerase II elongation kinetics to activate signal-induced transcription

Signal-induced transcriptional programs regulate critical biological processes through the precise spatiotemporal activation of Immediate Early Genes (IEGs); however, the mechanisms of transcription induction remain poorly understood. By combining an acute depletion system with high resolution genomics approaches to interrogate synchronized, temporal transcription, we reveal that KAP1/TRIM28 is a first responder that fulfills the temporal and heightened transcriptional demand of IEGs. Unexpectedly, acute KAP1 loss triggers an increase in RNA polymerase II elongation kinetics during early stimulation time points. This elongation defect derails the normal progression through the transcriptional cycle during late stimulation time points, ultimately leading to decreased recruitment of the transcription apparatus for re-initiation thereby dampening IEGs transcriptional output. Collectively, KAP1 plays a counterintuitive role by negatively regulating transcription elongation to support full activation across multiple transcription cycles of genes critical for cell physiology and organismal functions.

molecular biology↗

bioRxiv2024

Relaxin Modulates the Genomic Actions and Biological Effects of Estrogen in the Myometrium by Reducing Estrogen Receptor Alpha Phosphorylation

Estradiol (E2) and relaxin (Rln) are steroid and polypeptide hormones, respectively, with important roles in the female reproductive tract, including myometrium. Some actions of Rln, which are mediated by its membrane receptor RXFP1, require or are augmented by E2 signaling through its cognate nuclear steroid receptor, estrogen receptor alpha (ER). In contrast, other actions of Rln act in opposition to the effects of E2. Here we explored the molecular and genomic mechanisms that underlie the functional interplay between E2 and Rln in the myometrium. We used both ovariectomized female mice and immortalized human myometrial cells expressing wild-type or mutant ER (hTERT-HM-ER cells). Our results indicate that Rln modulates the genomic actions and biological effects of estrogen in the myometrium and myometrial cells by reducing phosphorylation of ER on serine 118 (S118), as well as by reducing the E2-dependent binding of ER across the genome. These effects were associated with changes in the hormone-regulated transcriptome, including a decrease in the E2-dependent expression of some genes and enhanced expression of others. The inhibitory effects of Rln cotreatment on the E2-dependent phosphorylation of ER required the nuclear dual-specificity phosphatases DUSP1 and DUSP5. Moreover, the inhibitory effects of Rln were reflected in a concomitant inhibition of the E2-dependent contraction of myometrial cells. Collectively, our results identify a pathway that integrates Rln/RXFP1 and E2/ER signaling, resulting in a convergence of membrane and nuclear signaling pathways to control genomic and biological outcomes.

molecular biology↗

bioRxiv2023

A PARP14/TARG1-Regulated RACK1 MARylation Cycle Drives Stress Granule Dynamics in Ovarian Cancer Cells

Mono(ADP-ribosyl)ation (MARylation) is emerging as a critical regulator of ribosome function and translation. Herein, we demonstrate that RACK1, an integral component of the ribosome, is MARylated on three acidic residues by the mono(ADP-ribosyl) transferase (MART) PARP14 in ovarian cancer cells. MARylation of RACK1 is required for stress granule formation and promotes the colocalization of RACK1 in stress granules with G3BP1, eIF3{eta}, and 40S ribosomal proteins. In parallel, we observed reduced translation of a subset of mRNAs, including those encoding key cancer regulators (e.g., AKT). Treatment with a PARP14 inhibitor or mutation of the sites of MARylation on RACK1 blocks these outcomes, as well as the growth of ovarian cancer cells in culture and in vivo. To re-set the system after prolonged stress and recovery, the ADP-ribosyl hydrolase TARG1 deMARylates RACK1, leading to the dissociation of the stress granules and the restoration of translation. Collectively, our results demonstrate a therapeutically targetable pathway that controls stress granule assembly and disassembly in ovarian cancer cells. SummaryWe have discovered a druggable PARP14/TARG1-regulated pathway that mediates site- specific mono(ADP-ribosyl)ation of RACK1, a ribosomal protein. This pathway controls stress granule assembly and disassembly, as well as the translation of a subset of mRNAs, to modulate the growth of ovarian cancer cells in culture and in vivo.

cell biology↗

bioRxiv2022

Functional Characterization of lncRNA152 as an Angiogenesis-Inhibiting Tumor Suppressor in Triple-Negative Breast Cancers

AO_SCPLOWBSTRACTC_SCPLOWLong non-coding RNAs have been implicated in many of the hallmarks of cancer. Herein, we found that the expression of lncRNA152 (lnc152; a.k.a. DRAIC), which we annotated previously, is highly upregulated in luminal breast cancer (LBC) and downregulated in triple-negative breast cancer (TNBC). Knockdown of lnc152 promotes cell migration and invasion in LBC cell lines. In contrast, ectopic expression of lnc152 inhibits growth, migration, invasion, and angiogenesis in TNBC cell lines. In mice, lnc152 inhibited the growth of TNBC cell xenografts, as well as metastasis of TNBC cells in an intracardiac injection model. Transcriptome analysis of the xenografts indicated that lnc152 downregulates genes controlling angiogenesis. Using pull down assays coupled with LC-MS/MS, we identified RBM47, a known tumor suppressor in breast cancer, as a lnc152-interacting protein. The effects of lnc152 in TNBC cells are mediated, in part, by regulating the expression of RBM47. Collectively, our results demonstrate that lnc152 is an angiogenesis-inhibiting tumor suppressor that attenuates the aggressive cancer-related phenotypes found in TNBC. SO_SCPLOWTATEMENTC_SCPLOWO_SCPCAP C_SCPCAPO_SCPLOWOFC_SCPLOW SO_SCPLOWIGNIFICANCEC_SCPLOWThis study identifies lncRNA152 as an angiogenesis-inhibiting tumor suppressor that attenuates the aggressive cancer-related phenotypes found in TNBC by upregulating the expression of the tumor suppressor RBM47. As such, lncRNA152 may serve as a biomarker to track aggressiveness of breast cancer, as well as therapeutic target for treating TNBC.

cancer biology↗