PHOSPHO1 Serves as a Key Metabolism-Related Biomarker in the Tumorigenesis of Diffuse Large B-cell Lymphoma.

OBJECTIVE: Diffuse large B-cell lymphoma (DLBCL) is an aggressive type of non-Hodgkin lymphoma. Due to its genetic heterogeneity and abnormal metabolism, many DLBCL patients have a poor prognosis. This study investigated the key metabolism-related genes and potential mechanisms. METHODS: Differentially expressed genes, differentially expressed transcription factors (TFs), and differentially expressed metabolism-related genes (DEMRGs) of glucose and lipid metabolic processes were identified using the edgeR package. Key DEMRGs were screened by Lasso regression, and a prediction model was constructed. The cell type identification by estimating relative subsets of RNA transcripts algorithm was utilized to assess the fraction of immune cells, and Gene Set Enrichment Analysis was used to determine immune-related pathways. A regulatory network was constructed with significant co-expression interactions among TFs, DEMRGs, immune cells/pathways, and hallmark pathways. RESULTS: A total of 1551 DEMRGs were identified. A prognostic model with a high applicability (area under the curve=0.921) was constructed with 13 DEMRGs. Tumorigenesis of DLBCL was highly related to the neutrophil count. Four DEMRGs (PRXL2AB, CCN1, DECR2 and PHOSPHO1) with 32 TF-DEMRG, 36 DEMRG-pathway, 14 DEMRG-immune-cell, 9 DEMRG-immune-gene-set, and 67 DEMRG-protein-chip interactions were used to construct the regulatory network. CONCLUSION: We provided a prognostic prediction model based on 13 DEMRGs for DLBCL. We found that phosphatase, orphan 1 (PHOSPHO1) is positively regulated by regulatory factor X5 (RFX5) and mediates MYC proto-oncogene (MYC) targeting the V2 pathway and neutrophils.

Improved HPLC method for the determination of ribavirin concentration in red blood cells and its application in patients with COVID-19.

Ribavirin is a synthetic, broad-spectrum antiviral drug. Ribavirin is recommended as an antiviral drug in the Interim Guidance for Diagnosis and Treatment (the seventh edition) of COVID-19. The ribavirin levels in red blood cells may be closely related to both its efficacy and adverse drug reactions. In this study, a simple and fast HPLC-UV method was established to determine the concentrations of total ribavirin in the red blood cells of 13 patients with COVID-19. Phosphorylated ribavirin was dephosphorylated by phosphatase incubation to obtain the total amount of ribavirin in red blood cells. The chromatographic column was an Atlantis C18 . The recoveries were 85.45-89.05% at three levels. A good linear response was from 1 to 200 µg/ml, with a correlation coefficient of r2 = 0.9991. The concentration of total ribavirin in the red blood cells of the patients ranged from 30.83 to 133.34 µg/ml. The same samples without phosphatase incubation ranged from 4.07 to 20.84 µg/ml. About 85% of ribavirin was phosphorylated in red blood cells. In addition, we observed changes in these patients' hematological parameters and found that the erythrocyte, hemoglobin and hematocrit declined to the lowest levels on the fifth day after discontinuation of ribavirin (p < 0.05).

Potential microbial bioindicators of phosphorus mining in a temperate deciduous forest.

AIMS: The soil microbial community plays a critical role in increasing phosphorus (P) availability in low-P, weathered soils by "mining" recalcitrant organic P through the production of phosphatase enzymes. However, there is a lack of data on the fungal and bacterial taxa which are directly involved in P mining, which could also serve as potential microbial bioindicators of low P availability. METHODS AND RESULTS: Leveraging a 5-year P enrichment experiment on low-P forest soils, high-throughput sequencing was used to profile the microbial community to determine which taxa associate closely with P availability. We hypothesized that there would be a specialized group of soil micro-organisms that could access recalcitrant P and whose presence could serve as a bioindicator of P mining. Community profiling revealed several candidate bioindicators of P mining (Russulales, Acidobacteria Subgroup 2, Acidobacteriales, Obscuribacterales and Solibacterales), whose relative abundance declined with elevated P and had a significant, positive association with phosphatase production. In addition, we identified candidate bioindicators of high P availability (Mytilinidales, Sebacinales, Chitinophagales, Cytophagales, Saccharimonadales, Opitulales and Gemmatales). CONCLUSIONS: This research provides evidence that mitigating P limitation in this ecosystem may be a specialized trait and is mediated by a few microbial taxa. SIGNIFICANCE AND IMPACT OF THE STUDY: Here, we characterize Orders of soil microbes associated with manipulated phosphorus availability in forest soils to determine bioindicator candidates for phosphorus. Likewise, we provide evidence that the microbial trait to utilize recalcitrant organic forms of P (e.g. P mining) is likely a specialized trait and not common to all members of the soil microbial community. This work further elucidates the role that a complex microbial community plays in the cycling of P in low-P soils, and provides evidence for future studies on microbial linkages to human-induced ecosystem changes.

Fluorogenic probes for imaging cellular phosphatase activity.

The ability to visualize enzyme activity in a cell, tissue, or living organism can greatly enhance our understanding of the biological roles of that enzyme. While many aspects of cellular signaling are controlled by reversible protein phosphorylation, our understanding of the biological roles of the protein phosphatases involved is limited. Here, we provide an overview of progress toward the development of fluorescent probes that can be used to visualize the activity of protein phosphatases. Significant advances include the development of probes with visible and near-infrared (near-IR) excitation and emission profiles, which provides greater tissue and whole-animal imaging capabilities. In addition, the development of peptide-based probes has provided some selectivity for a phosphatase of interest. Key challenges involve the difficulty of achieving sufficient selectivity for an individual member of a phosphatase enzyme family and the necessity of fully validating the best probes before they can be adopted widely.

Arbuscular mycorrhizal fungi and Trichoderma viride cooperative effect on biochemical, mineral content, and protein pattern of onion plants.

The benefits of growth-stimulating microbes in crop production represent great opportunities for recent agricultural practices. Thus, the present investigation deals with examining whether arbuscular mycorrhizal (AM) fungi or Trichoderma viride application or their dual inoculation could improve the biochemical parameters and mineral and nutrient contents of onion plants (Allium cepa) under glasshouse conditions. The results evidenced that both AM fungi and T. viride are compatible with each other, and their combined use is effective, not only in improving the biochemical parameters, such as total soluble carbohydrates, protein contents, total free amino acids, acid, and alkaline phosphatases, but also in increasing mineral and nutrient contents (N, P, K+ , Ca2+ , Mg2+ , and Zn) in onion plants, in which an increase of 67%, 49%, and 112% was observed in shoot onion P content with AM, T. viride, and with their dual inoculation, respectively, as compared with the controlled ones. Also, AM fungal colonization percentage augmented greatly with T. viride inoculation. Moreover, the protein profile of onion leaves revealed the appearance of newly protein bands with AM and T. viride applications. Therefore, their applications improved onion plant development, which could be used to replace the expensive chemical fertilizers, thus increasing onion quality.

Fluorescent probe displacement assays reveal unique nucleic acid binding properties of human nudix enzymes.

Nudix proteins are members of a large family of homologous enzymes that hydrolyze nucleoside diphosphates linked to other compounds. The substrates for a subset of Nudix enzymes are all nucleotides linked to RNA, like the m7G mRNA caps and the more recently discovered NAD(H) RNA caps. However, the RNA affinity and nucleic acid specificity of Nudix proteins has not yet been explored in depth. In this study we designed new fluorescence-based assays to examine the interaction of purified recombinant E. coli NudC and human Nudt1 (aka MTH1) Nudt3, Nudt12, Nudt16, and Nudt20 (aka Dcp2). All Nudix proteins except Nudt1 and Nudt12 bound both RNA and DNA stoichiometrically with high affinity (dissociation constants in the nanomolar range) and no clear sequence specificity. In stark contrast, Nudt12 binds RNA but not similar DNA oligonucleotides. Nudt12 also bound RNAs with 5' NAD+ caps more tightly than those with NADH or m7G cap. NudC was similarly selective against m7G caps but did not differentiate between NAD+ and NADH capped RNA. Nudt3, Nudt16, and Nudt20 bound m7G capped RNA more tightly than RNA with NADH caps.

Small Molecule as Fluorescent Probes for Monitoring Intracellular Enzymatic Transformations.

All cellular processes are the results of synchronized actions of several intracellular biochemical pathways. Recent emphasis is to visualize such pathways using appropriate small molecular reagents, dye-labeled proteins, and genetically encoded fluorescent biosensors that produce a luminescence ON response either on selective binding or on reacting with an analyte that is produced through a specific biochemical/enzymatic transformation. Studying such enzymatic processes by probing the fluorescence response as the read-out signal is expected to provide important insights into crucial biochemical transformations induced by an enzyme in its native form. Many of such studies are extended for monitoring enzymatic transformations under in vitro or in vivo condition. A few of the recent reports reveal that such molecular probes are even capable of quantifying abnormal levels of enzymes in real-time and is linked to the key area of clinical diagnostics and chemical biology. A synchronized analysis of all such reports helps in developing a rationale for designing purpose-built molecular probes or chemodosimeters as well as newer reagents for studying crucial enzymatic process or quantification of the respective enzyme. In this review, an attempt will be there to highlight several recent bioimaging reagents and studies that have provided insights into crucial biochemical or enzymatic transformations.

A supramolecular hydrogel to boost the production of antibodies for phosphorylated proteins.

Antibodies are widely used both in clinical practice and in research. However, the development of methods to increase the ratio of antibodies to recognize phosphorylated proteins remains challenging. In this study, we report a novel and useful method for the efficient production of antibodies for phosphorylated proteins. Based on our previously developed vaccine adjuvant Nap-GDFDFDY, we prepared hydrogels by the Ca2+-induced self-assembly of a phosphorylated peptide gelator Nap-GDFDFpDY. The hydrogel could protect phosphorylated antigens from being dephosphorylated by endogenous phosphatase, thus selectively increasing the ratio of the antibodies for phosphorylated proteins. Our study provides a useful strategy for the production of antibodies to recognize proteins with specific posttranslational modifications.

The voltage sensing phosphatase (VSP) localizes to the apical membrane of kidney tubule epithelial cells.

Voltage-sensing phosphatases (VSPs) are transmembrane proteins that couple changes in membrane potential to hydrolysis of inositol signaling lipids. VSPs catalyze the dephosphorylation of phosphatidylinositol phosphates (PIPs) that regulate diverse aspects of cell membrane physiology including cell division, growth and migration. VSPs are highly conserved among chordates, and their RNA transcripts have been detected in the adult and embryonic stages of frogs, fish, chickens, mice and humans. However, the subcellular localization and biological function of VSP remains unknown. Using reverse transcriptase-PCR (RT-PCR), we show that both Xenopus laevis VSPs (Xl-VSP1 and Xl-VSP2) mRNAs are expressed in early embryos, suggesting that both Xl-VSPs are involved in early tadpole development. To understand which embryonic tissues express Xl-VSP mRNA, we used in situ hybridization (ISH) and found Xl-VSP mRNA in both the brain and kidney of NF stage 32-36 embryos. By Western blot analysis with a VSP antibody, we show increasing levels of Xl-VSP protein in the developing embryo, and by immunohistochemistry (IHC), we demonstrate that Xl-VSP protein is specifically localized to the apical membrane of both embryonic and adult kidney tubules. We further characterized the catalytic activity of both Xl-VSP homologs and found that while Xl-VSP1 catalyzes 3- and 5-phosphate removal, Xl-VSP2 is a less efficient 3-phosphatase with different substrate specificity. Our results suggest that Xl-VSP1 and Xl-VSP2 serve different functional roles and that VSPs are an integral component of voltage-dependent PIP signaling pathways during vertebrate kidney tubule development and function.

Impact of long-term phosphorus fertilizer inputs on bacterial phoD gene community in a maize field, Northeast China.

The bacterial phoD gene encodes alkaline phosphomonoesterase, an enzyme which plays an important role in the release of plant-available inorganic phosphorus (P) from organic P in soil. However, the relationships between phoD gene community, alkaline phosphomonoesterase activity, and P availability in soil are poorly understood. In this study, we investigated how alkaline phosphomonoesterase activity, phoD gene abundance, and community structure are influenced by plant-available P using soils (0-10, 10-20 and 20-40 cm) from a long-term field trial in which a continuous maize (Zea mays L.) crop had received different levels of P fertilizer inputs (30, 60 kg P ha-1 year-1) for 28 years. Quantitative PCR and high-throughput sequencing were used to analyze phoD gene abundance and community composition. Alkaline phosphomonoesterase enzyme activity was negatively correlated with soil available P, which was reflected in corresponding data for phoD gene abundance. On the other hand, positive correlations were determined between phoD gene α-diversity and available P, while shifts in phoD gene community structure were related to changes in soil pH and P availability. The relative abundance of Pseudomonas was negatively correlated with P availability and positively correlated with alkaline phosphomonoesterase activity, suggesting that Pseudomonas may play an important role in soil organic P mineralization. The findings of this study demonstrated that changes of soil P availability as a result of long-term P fertilizer inputs significantly affected alkaline phosphomonoesterase activity by regulating phoD gene abundance, diversity, as well as altering the phoD gene community composition.

Specific Fluorescent Probe for Protein Histidine Phosphatase Activity.

Protein histidine phosphorylation plays a vital role in cell signaling and metabolic processes, and phosphohistidine (pHis) phosphatases such as protein histidine phosphatase 1 (PHPT1) and LHPP have been linked to cancer and diabetes, making them novel drug targets and biomarkers. Unlike the case for other classes of phosphatases, further studies of PHPT1 and other pHis phosphatases have been hampered by the lack of specific activity assays in complex biological mixtures. Previous methods relying on radiolabeling are hazardous and technically laborious, and small-molecule phosphatase probes are not selective toward pHis phosphatases. To address these issues, we herein report a fluorescent probe based on chelation-enhanced fluorescence (CHEF) to continuously measure the pHis phosphatase activity of PHPT1. Our probe exhibited excellent sensitivity and specificity toward PHPT1, enabling the first specific measurement of PHPT1 activity in cell lysates. Using this probe, we also obtained more physiologically relevant kinetic parameters of PHPT1, overcoming the limitations of previously used methods.

Synergism of Pseudomonas aeruginosa (LSE-2) nodule endophyte with Bradyrhizobium sp. (LSBR-3) for improving plant growth, nutrient acquisition and soil health in soybean.

The present study was aimed to assess the scope of native potential endophyte Pseudomonas aeruginosa (LSE-2) strain (KX925973) with recommended Bradyrhizobium sp. (LSBR-3) (KF906140) for synergistic effect to develop as consortium biofertilizer of soybean. A total of 28 non-rhizobial endophytic bacteria were isolated from cultivated and wild sp. of soybean. All isolates were screened for multifarious PGP traits viz. Indole-3-acetic acid (IAA), phosphate (P) and zinc (Zn) solubilization, siderophore, cell wall degrading enzymes and pathogenicity. Compatible of LSBR-3 and LSE-2 enhanced IAA, P-solubilization, 1-aminocyclopropane-carboxylate deaminase and biofilm formation over the single inoculant treatment. Further, consortium was evaluated in vivo for growth, symbiotic traits, nutrient acquisition, soil quality parameters and yield attributes of soybean. Improvement in growth parameters were recorded with dual inoculant LSBR-3 + LSE-2 as compared to LSBR-3 alone and un-inoculated control treatments. Significantly (p ≥ 0.05) high symbiotic and soil quality parameters (phosphatase and soil dehydrogenase activity) was recorded with LSBR-3 + LSE-2 at vegetative and flowering stage as compared to LSBR-3 alone and un-inoculated control treatments. Single inoculation of LSBR-3 improved grain yield by 4.25% over the un-inoculated control treatment, further, enhancement in yield was recorded with consortium inoculant (LSBR-3 and LSE-2) by 3.47% over the LSBR-3 alone. Application of consortium inoculant (LSBR-3 + LSE-2) gave an additional income of Rs. 5089/ha over the un-inoculated control treatment. The results, thus strongly suggest that endophytic diazotroph LSE-2 can be used as potent bio-inoculant along with LSBR-3 as bio-enhancer for improving soybean productivity in a sustainable system.

TULP3 is required for localization of membrane-associated proteins ARL13B and INPP5E to primary cilia.

The primary cilia are known as biosensors that transduce signals through the ciliary membrane proteins in vertebrate cells. The ciliary membrane contains transmembrane proteins and membrane-associated proteins. Tubby-like protein 3 (TULP3), a member of the tubby family, has been shown to interact with the intraflagellar transport-A complex (IFT-A) and to be involved in the ciliary localization of transmembrane proteins, although its role in the ciliary entry of membrane-associated proteins has remained unclear. Here, to determine whether TULP3 is required for the localization of ciliary membrane-associated proteins, we generated and analyzed TULP3-knockout (KO) hTERT RPE-1 (RPE1) cells. Immunofluorescence analysis demonstrated that ciliary formation was downregulated in TULP3-KO cells and that membrane-associated proteins, ADP-ribosylation factor-like 13B (ARL13B) and inositol polyphosphate-5-phosphatase E (INPP5E), failed to localize to primary cilia in TULP3-KO cells. These defects in the localization of ARL13B and INPP5E in TULP3-KO cells were rescued by the exogenous expression of wild-type TULP3, but not that of mutant TULP3 lacking the ability to bind IFT-A. In addition, the expression of TUB protein, another member of the tubby family whose endogenous expression is absent in RPE1 cells, also rescued the defective ciliary localization of ARL13B and INPP5E in TULP3-KO cells, suggesting that there is functional redundancy between TULP3 and TUB. Our findings indicate that TULP3 participates in ciliogenesis, and targets membrane-associated proteins to primary cilia via binding to IFT-A.

Influence of triazole pesticides on tillage soil microbial populations and metabolic changes.

Pesticides are generally applied to agricultural soil to control crop diseases, with the critical goal of preventing yield loss and optimizing economic returns. However, the excessive utilization of pesticides in agriculture is a severe environmental and human health problem. In the present study, effect of triazole based fungicide, propiconazole on soil physicochemical properties, stimulatory impact of propiconazole residue on soil microbial communities and soil enzyme activities (phosphatise and urease) in contaminated red sandy loam and deep black soils of paddy (Oryza sativa L.) fields at different concentrations were evaluated. The liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS/MS) analysis showed high levels of propiconazole residues of 434 and 426 ng g-1 in red sandy loam and deep black soils, respectively. A total of 27 bacterial and 18 fungal strains were isolated from propiconazole-contaminated soils, identified by molecular markers and had their sequences deposited in the GenBank. We observed a pronounced increase in soil microbial growth, and urease and phosphatase activities at lower propiconazole concentrations up to 2 weeks post-treatment. On the contrary, the microbial growth and urease and phosphatase activities were relentlessly reduced at higher propiconazole concentrations and a long incubation period after 2 to 4 weeks of post-treatment. Overall, it was concluded that the concentration-dependency and incubation period of propiconazole would enhance the growth and activity of soil microbes and enzymes respectively and the higher application will be detrimental to the soil health.

Global patterns of phosphatase activity in natural soils.

Soil phosphatase levels strongly control the biotic pathways of phosphorus (P), an essential element for life, which is often limiting in terrestrial ecosystems. We investigated the influence of climatic and soil traits on phosphatase activity in terrestrial systems using metadata analysis from published studies. This is the first analysis of global measurements of phosphatase in natural soils. Our results suggest that organic P (Porg), rather than available P, is the most important P fraction in predicting phosphatase activity. Structural equation modeling using soil total nitrogen (TN), mean annual precipitation, mean annual temperature, thermal amplitude and total soil carbon as most available predictor variables explained up to 50% of the spatial variance in phosphatase activity. In this analysis, Porg could not be tested and among the rest of available variables, TN was the most important factor explaining the observed spatial gradients in phosphatase activity. On the other hand, phosphatase activity was also found to be associated with climatic conditions and soil type across different biomes worldwide. The close association among different predictors like Porg, TN and precipitation suggest that P recycling is driven by a broad scale pattern of ecosystem productivity capacity.

Growth promotion of peanut (Arachis hypogaea L.) and maize (Zea mays L.) plants by single and mixed cultures of efficient phosphate solubilizing bacteria that are tolerant to abiotic stress and pesticides.

The aims of this study were, to analyze in vitro phosphate solubilization activity of six native peanut bacteria and to determine the effect of single and mixed inoculation of these bacteria on peanut and maize plants. Ability to produce organic acids and cofactor PQQ, to solubilize FePO4 and AlPO4 and phosphatase activity were analyzed. Also, the ability to solubilize phosphate under abiotic stress and in the presence of pesticides of the selected bacteria was determined. The effect of single and mixed bacterial inocula was analyzed on seed germination, maize plant growth and in a crop rotation plant assay with peanut and maize. The six strains produced gluconic acid and five released cofactor PQQ into the medium. All bacteria showed ability to solubilize phosphate from FePO4 and AlPO4 and phosphatase activity. The ability of the bacteria to solubilize tricalcium phosphate under abiotic stress and in presence of pesticides indicated encouraging results. Bacterial inoculation on peanut and maize increased seed germination, plant́s growth and P content. Phosphate solubilizing bacteria used in this study showed efficient phosphate mineralizing and solubilization ability and would be potential P-biofertilizers for peanut and maize.

Integrated Strategies to Gain a Systems-Level View of Dynamic Signaling Networks.

In order to survive and function properly in the face of an ever changing environment, cells must be able to sense changes in their surroundings and respond accordingly. Cells process information about their environment through complex signaling networks composed of many discrete signaling molecules. Individual pathways within these networks are often tightly integrated and highly dynamic, allowing cells to respond to a given stimulus (or, as is typically the case under physiological conditions, a combination of stimuli) in a specific and appropriate manner. However, due to the size and complexity of many cellular signaling networks, it is often difficult to predict how cellular signaling networks will respond under a particular set of conditions. Indeed, crosstalk between individual signaling pathways may lead to responses that are nonintuitive (or even counterintuitive) based on examination of the individual pathways in isolation. Therefore, to gain a more comprehensive view of cell signaling processes, it is important to understand how signaling networks behave at the systems level. This requires integrated strategies that combine quantitative experimental data with computational models. In this chapter, we first examine some of the progress that has recently been made toward understanding the systems-level regulation of cellular signaling networks, with a particular emphasis on phosphorylation-dependent signaling networks. We then discuss how genetically targetable fluorescent biosensors are being used together with computational models to gain unique insights into the spatiotemporal regulation of signaling networks within single, living cells.

Functional identification of a novel transcript variant of INPP4B in human colon and breast cancer cells.

The 4-phosphatase Inositol polyphosphate 4-phosphatase II (INPP4B) is a regulator of the PI3K signalling pathway and functions to suppress or promote activation of downstream kinases depending on cell type and context. Here we report the identification of a novel small transcript variant of INPP4B (INPP4B-S) that has a role in promoting proliferation of colon and breast cancer cells. INPP4B-S differed from full length INPP4B (INPP4B-FL) by the insertion of a small exon between exons 15 and 16 and the deletion of exons 20-24. Nevertheless, INPP4B-S retained all the functional domains of INPP4B-FL and was similarly located to the cytoplasm. Overexpression of INPP4B-S increased, whereas selective knockdown of INPP4B-S reduced the rate of proliferation in HCT116 and MCF-7 cells. These results warrant further investigation of the role INPP4B-S in activation of downstream kinases and in regulation of cancer pathogenesis.

The influences of four types of soil on the growth, physiological and biochemical characteristics of Lycoris aurea (L' Her.) Herb.

Based on the characteristics of Lycoris aurea (L. aurea) natural distribution and local soil types, we selected four representative types of soil, including humus soil, sandy soil, garden soil and yellow-brown soil, for conducting the cultivation experiments to investigate key soil factors influencing its growth and development and to select the soil types suitable for cultivating it. We found that there existed significant differences in the contents of mineral elements and the activities of soil enzymes (urease, phosphatase, sucrase and catalase) etc. Among which, the contents of organic matters, alkali-hydrolysable nitrogen, Ca and Mg as well as the activities of soil enzymes in humus soil were the highest ones. In yellow-brown soil, except for Fe, the values of all the other items were the lowest ones. Net photosynthetic rate (Pn), biomass and lycorine content in humus soil were all the highest ones, which were increased by 31.02, 69.39 and 55.79%, respectively, as compared to those of yellow-brown soil. Stepwise multiple regression analysis and path analysis indicated that alkali-hydrolysable nitrogen, and Ca etc. were key soil factors influencing Pn, biomass and lycorine content of L. aurea. Thus, humus soil can be used as medium suitable for artificial cultivation of L. aurea.

Basal biomarkers nestin and INPP4b identify intrinsic subtypes accurately in breast cancers that are weakly positive for oestrogen receptor.

AIMS: Recent evidence indicates that weakly positive immunohistochemical staining of oestrogen receptor (ER) is not associated reliably with a luminal subtype, with the majority reclassified as basal-like by gene expression profile. In this study we assessed the capacity of recently identified immunohistochemical markers of basal-like subtype not dependent upon ER status - positive expression of nestin or loss of inositol polyphosphate-4-phosphatase (INPP4b) - to discriminate intrinsic subtypes, focusing on clinically problematic cases with weak ER positivity. METHODS AND RESULTS: Formalin-fixed paraffin-embedded blocks, enriched for large proportions of ER-negative and ER weakly positive breast cancers, were selected from two previous studies conducted in the period 2008-13 and used for (i) RNA extraction for 50-gene subtype predictor (PAM50) intrinsic subtyping and (ii) tissue microarray construction for immunohistochemical assessment of nestin and INPP4b. Fifty-eight cases were weakly positive for ER (Allred 3-5), among which 28 (48%) were assigned as basal-like by PAM50 gene expression. In these 58 cases, the nestin/INPP4b panel identified 23 basal-like cases with a positive predictive value of 87% [95% confidence interval (CI) 78-95%] and excluded luminal subtype with a negative predictive value of 95% (95% CI 88-100%). Weakly positive ER patients assigned as basal-like by nestin/INPP4b definition demonstrated a median survival time of 45.8 months, significantly lower than 65 months among other ER weakly positive cases (P = 0.012). CONCLUSIONS: Immunohistochemical assessment of nestin and INPP4b provides an accurate, accessible and inexpensive tool to identify basal-like breast cancer subtype in the clinically problematic setting of weak ER positivity. This panel identifies poor prognosis patients who might need strong considerations for non-endocrine-based therapies.