Biology subjects

Sahin, O.

Publications and source records attributed to Sahin, O..

17 recordsLinked to original sources

bioRxiv2026

A preclinical platform for focused ultrasound delivery from microplate to awake brain

Background. Focused ultrasound (FUS) has broad therapeutic potential, but its mechanisms of action are poorly understood. Preclinical FUS research enables rigorous interrogation of understudied parameters, but fragmented, single-purpose benchtop devices prevent standardized acoustic exposure across models. Objective. To describe a unified preclinical FUS platform for cell culture, ex vivo tissue, and awake stereotaxic in vivo delivery in one lightweight system, validated using glioblastoma as a disease model. Methods. We performed single-well FUS delivery to 96-well microplates, single-well delivery to freshly resected human glioblastoma tissue, and stereotaxic transcranial delivery to awake, head-fixed mice ambulating freely on a floating cage. Output was independently calibrated in free field, with measured microplate insertion loss. Pulsed low-intensity focused ultrasound (pLIFU) was applied to GL261-bearing mice, resected human glioblastoma, and macrophage cell lines. Results. Awake stereotaxic pLIFU produced acute tumor signal attenuation in GL261-bearing mice (mean log2 fold-change -1.66 versus +5.20 controls, p = 0.016) with bioluminescence evidence consistent with focal targeting. Ex vivo pLIFU produced directionally consistent immunophenotypic shifts in human glioblastoma (increased iNOS+, decreased Arg1+ populations). In vitro, pLIFU reduced CD80 on immunosuppressive macrophages to 73% of baseline in RAW 264.7 cells (p = 0.0008, n = 5) and 64% in THP-1 cells (p = 0.0006, n = 2), with MHC II upregulation in RAW 264.7 (ratio 1.65, p = 0.004) and ARG1 reduction in THP-1 (ratio 0.52, p = 0.0025). Conclusions. A unified preclinical FUS platform validated across in vitro, ex vivo, and awake in vivo applications enables stereotaxically guided transcranial FUS in awake, head-fixed mice ambulating in an exploratory manner during sonication, and single-well microplate treatments.

neuroscience↗

bioRxiv2026

TACC3-driven translation reprogramming dictates susceptibility or tolerance to mitotic stress

Translation reprogramming is central to cancer cell plasticity under stress. However, the molecular players coordinating translation and epitranscriptomic rewiring to determine adaptive responses to mitotic stress remain elusive. Here, we found that microtubule targeting agent (MTA)-induced CDK1 blocks global translation while it phosphorylates and degrades TACC3, a multifunctional adaptor, releasing eIF4A/eIF4E/eIF4G2 initiation factors. This promotes selective m7G cap-dependent translation of mRNAs with MTAup motif that are functionally required for apoptosis by disrupting proteostasis, promoting MTA-sensitivity. On the other hand, selectively translated TACC3 interacts with eIF3d/eIF4G1 and the m6A writer METTL3, mediating switch to m6A methylation and m7G cap-independent translation of mRNAs with hnRNPC-motif involved in chromosome segregation, driving MTA tolerance. TACC3 inhibition overcomes MTA resistance via restoring translation reprogramming. These findings demonstrate that TACC3 is a pivotal coordinator of translation/epitranscriptomic reprogramming and a therapeutic target in MTA-refractory cancers.

cancer biology↗

bioRxiv2026

Lysyl oxidase drives ccRCC progression by coordinating HIF-2α transcription program with tumor microenvironment

Clear cell renal cell carcinoma (ccRCC) is driven by persistent HIF-2 transcription program initiated by VHL loss, yet molecular mediators sustaining this program are poorly defined. Using single-cell transcriptomics, we identified lysyl oxidase (LOX) as a driver of ccRCC progression, selectively enriched in a hypoxia/epithelial-mesenchymal transition (EMT) gene program associated with poor outcome. While LOX oxidizes and stabilizes HIF-2 by antagonizing HUWE1-mediated ubiquitination and degradation, thereby sustaining HIF-2-driven transcription in cancer cells, it also remodels extracellular matrix (ECM) and promotes angiogenesis in the tumor microenvironment (TME). Genetic or pharmacological inhibition of LOX destabilizes HIF-2, disrupts ECM, inhibits angiogenesis, and suppresses tumor initiation, growth, and metastasis in vivo. LOX inhibition enhances anti-angiogenic therapy response and remains effective in belzutifan-resistant HIF-2 G323E-mutant tumors. Nuclear LOX protein correlates with nuclear HIF-2 in high-grade patient tumors. Together, LOX coordinates HIF-2 transcription program with TME and is a therapeutic target in ccRCC.

cancer biology↗

bioRxiv2025

Single-Cell Microwave Cytometry for Drug Resistance Detection in Cancer

Monitoring biophysical changes in single cells induced by drugs is crucial for advancing cancer therapies, especially for highly heterogeneous tumours. Emerging methods for single-cell drug sensitivity testing have largely relied on phenomenological analyses. Here, we present a novel electronic cytometry platform integrating microwave resonators with impedance cytometry, enabling simultaneous, label-free measurements of cell volume and dielectric permittivity at microwave frequencies. This approach uniquely captures intracellular differential responses indicative of drug-induced biophysical states, thus providing deeper insights beyond traditional phenomenological analyses. We first validated the platform using varying salt concentrations. We then demonstrated that the sensor platform could differentiate between drug resistant versus sensitive phenotypes in multiple isogenic cancer cell lines treated with cytostatic, cytotoxic and mixed-effect drugs. Notably, we showed that the technique performs successfully in patient-derived tumor organoids, a model system highlighting its immediate clinical relevance. Our findings underscore the potential of electronic measurements at the single cell level to provide informative and actionable biophysical signals relating to cellular drug response. The implementation of this platform could significantly advance cancer treatment by identifying the resistant cell populations in heterogenous tumours and optimizing selection of drugs for each patient, paving the way towards precision medicine.

bioengineering↗

bioRxiv2024

The epithelial adherens junction component PLEKHA7 regulates ECM remodeling and cell behavior through miRNA-mediated regulation of MMP1 and LOX

Epithelial adherens junctions (AJs) are cell-cell adhesion complexes that are influenced by tissue mechanics, such as those emanating from the extracellular matrix (ECM). Here, we introduce a mechanism whereby epithelial AJs can also regulate the ECM. We show that the AJ component PLEKHA7 regulates levels and activity of the key ECM remodeling components MMP1 and LOX in well-differentiated colon epithelial cells, through the miR-24 and miR-30c miRNAs. PLEKHA7 depletion in epithelial cells results in LOX-dependent ECM remodeling in culture and in the colonic mucosal lamina propria in mice. Furthermore, PLEKHA7-depleted cells exhibit increased migration and invasion rates that are MMP1- and LOX-dependent, and form colonies in 3D cultures that are larger in size and acquire aberrant morphologies in stiffer matrices. These results reveal an AJ-mediated mechanism, through which epithelial cells drive ECM remodeling to modulate their behavior, including acquisition of phenotypes that are hallmarks of conditions such as fibrosis and tumorigenesis. TeaserEpithelial cells instruct ECM remodeling to modulate their behavior, as a result of adherens junction and miRNA disruption.

cell biology↗

bioRxiv2023

Targeting LINC00152 activates cAMP/Ca2+/ferroptosis axis and overcomes tamoxifen resistance in ER+ breast cancer

Tamoxifen has been the mainstay therapy to treat early, locally advanced, and metastatic estrogen receptor-positive (ER+) breast cancer, constituting around 75% of all cases. However, emergence of resistance is common, necessitating the identification of novel therapeutic targets. Here, we demonstrated that long-noncoding RNA LINC00152 confers tamoxifen resistance via blocking tamoxifen-induced ferroptosis, an iron-mediated cell death. Mechanistically, inhibiting LINC00152 reduces the mRNA stability of phosphodiesterase 4D (PDE4D), leading to activation of cAMP/PKA/CREB axis and increased expression of TRPC1 Ca2+ channel. This causes cytosolic Ca2+ overload and generation of reactive oxygen species (ROS) that is, on one hand, accompanied by downregulation of FTH1, a member of the iron sequestration unit, thus increasing intracellular Fe2+ levels; and on the other hand, inhibition of the peroxidase activity upon reduced GPX4 and xCT levels. These ultimately induce lipid peroxidation and ferroptotic cell death in combination with tamoxifen. Overexpressing PDE4D rescues LINC00152 inhibition-mediated tamoxifen sensitization by de-activating the cAMP/Ca2+/ferroptosis axis. Importantly, high LINC00152 expression is significantly correlated with high PDE4D/low ferroptosis and worse survival in multiple cohorts of tamoxifen- or tamoxifen-containing endocrine therapy-treated ER+ breast cancer patients. Overall, we identified LINC00152 inhibition as a novel mechanism of ferroptosis induction and tamoxifen sensitization, thereby revealing LINC00152 and its effectors as actionable therapeutic targets to improve clinical outcome in refractory ER+ breast cancer.

cancer biology↗

bioRxiv2023

Reviving immunogenic cell death upon targeting TACC3 enhances T-DM1 response in HER2-positive breast cancer

Immunogenic cell death (ICD), an immune-priming form of cell death, has been shown to be induced by several different anti-cancer therapies. Despite being the first and one of the most successful antibody-drug conjugates (ADCs) approved for refractory HER2-positive breast cancer, little is known if response and resistance to trastuzumab emtansine (T-DM1) involves ICD modulation that can be leveraged to enhance T-DM1 response. Here, we report that T-DM1 induces spindle assembly checkpoint (SAC)-dependent ICD in sensitive cells by inducing eIF2 phosphorylation, surface exposure of calreticulin, ATP and HMGB1 release, and secretion of ICD-related cytokines, all of which are lost in resistance. Accordingly, an ICD-related gene signature correlates with clinical response to T-DM1-containing therapy. We found that transforming acidic coiled-coil containing 3 (TACC3) is overexpressed in T-DM1 resistant cells, and that T-DM1 responsive patients have reduced TACC3 protein while the non-responders exhibited increased TACC3 expression during T-DM1 treatment. Notably, genetic or pharmacological inhibition of TACC3 revives T-DM1-induced SAC activation and induction of ICD markers in vitro. Finally, TACC3 inhibition elicits ICD in vivo shown by vaccination assay, and it potentiates T-DM1 by inducing dendritic cell (DC) maturation and enhancing infiltration of cytotoxic T cells in the human HER2-overexpressing MMTV.f.huHER2#5 (Fo5) transgenic model. Together, our results show that ICD is a key mechanism of action of T-DM1 which is lost in resistance, and that targeting TACC3 restores T-DM1-mediated ICD and overcomes resistance. Statement of SignificanceImmunogenic cell death (ICD) is a novel mechanism of T-DM1 cytotoxicity that is lost upon T-DM1 resistance. Targeting TACC3 reinstates T-DM1-induced ICD, thus representing an attractive strategy to overcome T-DM1 resistance.

cancer biology↗

bioRxiv2022

Hexokinase 1b is a novel target for non-small-cell lung cancer

Deregulation of glycolysis is common in non-small cell lung cancer (NSCLC). Hexokinase (HK) enzymes catalyze the phosphoryl-group-transfer in glucose metabolism. There are a very few studies that have begun to reveal the connections between glucose metabolism and splicing programs. Unlike HK2 gene, which is expressed as a single transcript, there are several transcripts of the HK1 gene due to alternative splicing. However, the functional differential roles of HK1 isoforms in glucose metabolism and tumor progression are still elusive. Here, we show that primary NSCLC patient tumor cells metabolically differ from the normal lung epithelium where they display predominant expression of one of the HK1 transcripts, hexokinase1b (HK1b). We utilized CRISPR-Cas9 system to selectively target specific HK1b isoform in NSCLC and show that silencing HK1b in NSCLC cells inhibits tumorigenesis through diminishing glycolysis and proliferation. Our findings constitute the first demonstration of the first biochemical distinction between the HK1 splice variants. Finally, HK1b deletion sensitizes NSCLC cells to standard-of-care, cisplatin treatment, and the combination therapy synergistically increases both apoptotic cell death by cisplatin and autophagic cell death by increased formation of LC3-II associated autophagic vesicles and myelinoid bodies. Notably, loss of HK1b leads to cellular DNA damage, further combination with cisplatin therapy showed significantly increased levels of DNA damage. Importantly, we showed that glycolysis and cisplatin resistance can be restored by adding-back HK1b in HK1b knock-out cells. Our findings reveal that targeting HK1b isoform alone or in combination with cisplatin may represent a novel strategy for NSCLC patients.

cancer biology↗

bioRxiv2022

Targeting TACC3 represents a novel vulnerability in highly aggressive breast cancers with centrosome amplification

Centrosome amplification (CA) is a hallmark of cancer that is strongly associated with highly aggressive disease and worse clinical outcome. However, there are no effective strategies targeting cancer cells with CA while sparing normal cells. Here, we identified Transforming Acidic Coiled-Coil Containing Protein 3 (TACC3) to be overexpressed in tumors with CA, and its high expression is associated with dramatically worse clinical outcome. We demonstrated that TACC3 forms distinct functional interactions in mitotic and non-mitotic cancer cells with CA to facilitate centrosome clustering (CC) and transcriptional repression of tumor suppressors, respectively. We showed, for the first time, that TACC3 interacts with the Kinesin Family Member C1 (KIFC1) via its TACC domain in mitotic cells with CA and inhibition of TACC3 blocks this interaction, leading to apoptosis via multipolar spindle formation and activation of spindle assembly checkpoint (SAC)/CDK1/p-Bcl2 axis. In interphase, TACC3 interacts with the members of the nucleosome remodeling and deacetylase (NuRD) complex (HDAC2 and MBD2) in nucleus, and its inhibition causes p53-independent G1 arrest and apoptosis by blocking these interactions and activating the transcription of key tumor suppressors (e.g., p21, p16 and APAF1). Notably, inducing CA by chemical (cytochalasin D) or genomic (PLK4 overexpression or p53 loss) modulations renders cancer cells highly sensitive to TACC3 inhibition. Targeting TACC3 by small molecule inhibitors or guide RNAs strongly inhibits growth of organoids and breast cancer cell line- and patient-derived xenografts with CA. Altogether our results pave the way towards therapeutic targeting of TACC3 in highly aggressive cancers.

cancer biology↗

bioRxiv2021

A model screening pipeline for bile acid converting anti-Clostridioides difficile bacteria reveals unique biotherapeutic potential of Peptacetobacter hiranonis

Clostridioides difficile is an antibiotic-resistant bacterium that causes serious, toxin-mediated enteric disease in humans and animals. Gut dysbiosis and resultant alterations in the intestinal bile acid profile play an important role in the pathogenesis of C. difficile infection (CDI). Restoration of the gut microbiota and re-establishment of bacterial bile acid metabolism using fecal microbiota transplantation (FMT) has been established as a promising strategy against this disease, although this method has several limitations. Thus, a more defined and precise microbiota-based approach using bacteria that biotransform primary bile acids into secondary bile acids could effectively overcome these limitations and control CDI. Therefore, a screening pipeline was developed to isolate bile acid converting bacteria from fecal samples. Dogs were selected as a model CDI-resistant microbiota donor for this pipeline, which yielded a novel Peptacetobacter hiranonis strain that possesses unique anti-C. difficile properties, and both bile acid deconjugation and 7- dehydroxylating activities to perform bile acid conversion. The screening pipeline included a set of in vitro tests along with a precision in vivo gut colonization and bile acid conversion test using altered Schadler flora (ASF) colonized mice. In addition, this pipeline also provided essential information on the growth requirements for screening and cultivating the candidate bacterium, its survival in a CDI predisposing environment, and potential pathogenicity. The model pipeline documented here yielded multiple bile acid converting bacteria, including a P. hiranonis isolate with unique anti-C. difficile biotherapeutic potential, which can be further tested in subsequent preclinical and human clinical trials.

microbiology↗

bioRxiv2021

Coordinated regulation of WNT/β-catenin, c-Met, and Integrin signalling pathways by miR-193b controls triple negative breast cancer metastatic traits

BackgroundTriple Negative Breast Cancer (TNBC) is the most aggressive subtype of Breast Cancer (BC). Treatment options for TNBC patients are limited and further insights into disease aetiology are needed to develop better therapeutic approaches. microRNAs ability to regulate multiple targets could hold a promising discovery approach to pathways relevant for TNBC aggressiveness. Thus, we address the role of miRNAs in controlling signalling pathways and phenotypes relevant to the biology of TNBC. MethodsTo identify miRNAs regulating WNT/{beta}-catenin, c-Met, and integrin signalling pathways, we performed a high-throughput targeted proteomic approach, investigating the effect of 800 miRNAs on the expression of 62 proteins in the MDA-MB-231 TNBC cell line. We then developed a novel network analysis, Pathway Coregulatory (PC) score, to detect miRNAs regulating the three pathways. Using in vitro assays for cell growth, migration, apoptosis, and stem-cell content, we validated the function of candidate miRNAs. Bioinformatic analyses using BC patients datasets were employed to assess expression of miRNAs as well as their pathological relevance in TNBC patients. ResultsWe identified six candidate miRNAs coordinately regulating the three signalling pathways. Quantifying cell growth of three TNBC cell lines upon miRNA gain-of-function experiments, we characterised miR-193b as a strong and consistent repressor of this phenotype. Importantly, the effects of miR-193b were stronger than chemical inhibition of the individual pathways. We further demonstrated that miR-193b induced apoptosis, repressed migration, and regulated stem-cell markers in MDA-MB-231 cells. Furthermore, miR-193b expression was the lowest in patients classified as TNBC or Basal compared to other subtypes when classified by PAM50 signatures. Gene Set Enrichment Analysis showed that miR-193b expression was significantly associated with reduced activity of of WNT/{beta}-catenin and c-Met signalling pathways in TNBC patients. ConclusionsIntegrating miRNA-mediated effects and protein functions on networks, we show that miRNAs predominantly act in a coordinated fashion to activate or repress signalling pathways responsible for metastatic traits in TNBC. We further demonstrate that our top candidate, miR-193b, regulates these phenotypes to an extent stronger than individual pathway inhibition, thus proving that its effect on TNBC aggressiveness is mediated by repressing multiple interconnected pathways.

cancer biology↗

bioRxiv2020

Extreme stiffness of neuronal synapses and implications for synaptic adhesion and plasticity

Synapses play a critical role in neural circuits, and they are potential sites for learning and memory. Maintenance of synaptic adhesion is critical for neural circuit function, however, biophysical mechanisms that help maintain synaptic adhesion are not clear. Studies with various cell types demonstrated the important role of stiffness in cellular adhesions. Although synaptic stiffness could also play a role in synaptic adhesion, stiffnesses of synapses are difficult to characterize due to their small size and challenges in verifying synapse identity and function. To address these challenges, we have developed an experimental platform that combines atomic force microscopy, fluorescence microscopy, and transmission electron microscopy. Here, using this platform, we report that functional, mature, excitatory synapses had an average elastic modulus of approximately 200 kPa, two orders of magnitude larger than that of the brain tissue, suggesting stiffness might have a role in synapse function. Similar to various functional and anatomical features of neural circuits, synaptic stiffness had a lognormal-like distribution, hinting a possible regulation of stiffness by processes involved in neural circuit function. In further support of this possibility, we observed that synaptic stiffness was correlated with spine size, a quantity known to correlate with synaptic strength. Using established stages of the long-term potentiation timeline and theoretical models of adhesion cluster dynamics, we developed a biophysical model of the synapse that not only explains extreme stiffness of synapses, their statistical distribution, and correlation with spine size, but also offers an explanation to how early biomolecular and structural changes during functional potentiation could lead to strengthening of synaptic adhesion. According to this model, synaptic stiffness serves as an indispensable physical messenger, feeding information back to synaptic adhesion molecules to facilitate maintenance of synaptic adhesion.

biophysics↗

bioRxiv2020

Thymidylate synthase drives the phenotypes of epithelial-to-mesenchymal transition in non-small cell lung cancer

BackgroundEpithelial-to-mesenchymal transition (EMT) enhances motility, stemness and chemoresistance of carcinomas and is an important determinant of metastasis. Little is known about how various pathways coordinate to elicit EMTs different functional aspects. Even lesser has been studied in this context in non-small cell lung cancer (NSCLC), where EMT is a key event during early tumorigenesis. Thymidylate synthase (TS), a proliferation enzyme, has been previously correlated with EMT transcription factor ZEB1 in NSCLC and is associated with resistance against anti-folate chemotherapy. In this study we establish a functional correlation between TS, EMT, chemotherapy and metastasis and identify a network that might propel the TS mediated EMT phenotype. MethodsPublished datasets were analysed to evaluate significance of TS in NSCLC fitness and prognosis. mCherry based promoter reporter assay was used to sort Calu-1 and A549 NSCLC cells in TSHIGH and TSLOW. Metastatic potential of TS knock-down was assayed in syngeneic C57BL/6 mice. ResultsLow TS levels were prognostic and predicted chemotherapy response. NSCLC cell lines with higher TS promoter activity were more mesenchymal-like. RNA-seq from these cells, and shRNA mediated TS knocked down cells, identified EMT as one of the most differentially regulated pathways. EMT transcription factors HOXC6 and HMGA2 were identified as upstream regulator of TS whereas, AXL, SPARC and FOSL1 were identified as downstream effectors. TS knock-down reduced the metastatic colonisation in vivo. ConclusionThese results establish the role of TS as a theranostic NSCLC marker integrating survival, chemo-resistance and EMT, and identifies a regulatory network that could be exploited to target EMT-driven NSCLC.

cancer biology↗

bioRxiv2019

Genetic characterization of Streptococcus equi subspecies zooepidemicus associated with high swine mortality in United States

High mortality events due to Streptococcus equi subspecies zooepidemicus (S. zooepidemicus) in swine have not previously been reported in the United States. In September and October 2019, outbreaks with swine mortality up to 50% due to S. zooepidemicus septicemia were reported in Ohio and Tennessee. Genomic epidemiological analysis revealed that the eight outbreak isolates were clustered together with ATCC 36246, a Chinese strain caused outbreaks with high mortality, also closely related to three isolates from human cases from Virginia, but significantly different from an outbreak-unrelated swine isolate from Arizona and most isolates from other animal species. Comparative genomic analysis on two outbreak isolates and another outbreak-unrelated isolate identified several genomic islands and virulence genes specifically in the outbreak isolates only, which are likely associated with the high mortality observed in the swine population. These findings have implications for understanding, tracking, and possibly preventing diseases caused by S. zooepidemicus in swine.

microbiology↗

bioRxiv2018

Thymidylate synthase maintains the de-differentiated state of aggressive breast cancers

Cancer cells frequently boost nucleotide metabolism (NM) to support their increased proliferation, but the consequences of elevated NM on tumor de-differentiation are mostly unexplored. Here, we identified a role for thymidylate synthase (TS), a NM enzyme and established drug target, in cancer cell de-differentiation and investigated its clinical significance in breast cancer (BC). In vitro, TS knockdown increased the population of CD24+ differentiated cells, and attenuated migration and sphere-formation. RNA-seq profiling indicated a repression of epithelial-to-mesenchymal transition (EMT) signature genes upon TS knockdown, and TS-deficient cells showed an increased ability to invade and metastasize in vivo, consistent with the occurrence of a partial EMT phenotype. Mechanistically, TS enzymatic activity was found essential for the maintenance of the EMT/stem-like state by fueling a DPYD-dependent pyrimidine catabolism. In patient tissues, TS levels were found significantly higher in poorly differentiated and in triple negative BC (TNBC), and strongly correlated with worse prognosis. The present study provides the rationale to study in-depth the role of NM at the crossroads of proliferation and differentiation, and depicts new avenues for the design of novel drug combinations for the treatment of BC.

cancer biology↗

bioRxiv2018

Myosin filaments reversibly generate large forces in cells

We present high resolution experiments performed on elementary contractile units in cells that challenge our current understanding of molecular motor force generation. The key features are the development of a force per motor considerably larger than forces measured in single molecule experiments, a force increase followed by relaxation controlled by a characteristic displacement rather than by a characteristic force, the observation of steps at half the actin filament period even though a large number of motors are at work in an elementary contractile unit. We propose a generic two-state model of molecular motor collections with hand-over-hand contractions and we find that these unexpected observations are spontaneously emerging features of a collective motor behavior.

biophysics↗

bioRxiv2017

Discovering Competing Endogenous RNA Interactions in Breast Cancer Molecular Subtypes

MotivationLong non-coding RNAs(lncRNAs) can indirectly regulate mRNAs expression levels by sequestering microRNAs (miRNAs), and act as competing endogenous RNAs (ceRNAs) or as sponges. Previous studies identified lncRNA-mediated sponge interactions in various cancers including the breast cancer. However, breast cancer subtypes are quite distinct in terms of their molecular profiles; therefore, ceRNAs are expected to be subtype-specific as well.\n\nResultsTo find lncRNA-mediated ceRNA interactions in breast cancer subtypes, we develop an integrative approach. We conduct partial correlation analysis and kernel independence tests on patient gene expression profiles and further refine the candidate interactions with miRNA target information. We find that although there are sponges common to multiple subtypes, there are also distinct subtype-specific interactions. Functional enrichment of mRNAs that participate in these interactions highlights distinct biological processes for different subtypes. Interestingly, some of the ceRNAs also reside in close proximity in the genome; for example, those involving HOX genes, HOTAIR, miR-196a-1 and miR-196a-2. We also discover subtype-specific sponge interactions with high prognostic potential. For instance, when grouping is based on the expression patterns of specific sponge interactions, patients differ significantly in their survival distributions. If on the other hand, patients are grouped based on the individual RNA expression profiles of the sponge participants, they do not exhibit a significant difference in survival. These results can help shed light on subtype-specific mechanisms of breast cancer, and the methodology developed herein can help uncover sponges in other diseases.

bioinformatics↗