Yin P. Hung

A genetically encoded fluorescent reporter of ATP:ADP ratio

We constructed a fluorescent sensor of adenylate nucleotides by combining a circularly permuted variant of GFP with a bacterial regulatory protein, GlnK1, from Methanococcus jannaschii. The sensors affinity for Mg-ATP was <100 nM, as seen for other members of the bacterial PII regulator family, a surprisingly high affinity given that normal intracellular ATP concentration is in the millimolar range. ADP bound the same site of the sensor as Mg-ATP, competing with it, but produced a smaller change in fluorescence. At physiological ATP and ADP concentrations, the binding site is saturated, but competition between the two substrates causes the sensor to behave as a nearly ideal reporter of the ATP:ADP concentration ratio. This principle for sensing the ratio of two analytes by competition at a high-affinity site probably underlies the normal functioning of PII regulatory proteins. The engineered sensor, Perceval, can be used to monitor the ATP:ADP ratio during live-cell imaging.

Imaging Cytosolic NADH-NAD+ Redox State with a Genetically Encoded Fluorescent Biosensor

NADH is a key metabolic cofactor whose sensitive and specific detection in the cytosol of live cells has been difficult. We constructed a fluorescent biosensor of the cytosolic NADH-NAD(+) redox state by combining a circularly permuted GFP T-Sapphire with a bacterial NADH-binding protein, Rex. Although the initial construct reported [NADH] × [H(+)] / [NAD(+)], its pH sensitivity was eliminated by mutagenesis. The engineered biosensor Peredox reports cytosolic NADH:NAD(+) ratios and can be calibrated with exogenous lactate and pyruvate. We demonstrated its utility in several cultured and primary cell types. We found that glycolysis opposed the lactate dehydrogenase equilibrium to produce a reduced cytosolic NADH-NAD(+) redox state. We also observed different redox states in primary mouse astrocytes and neurons, consistent with hypothesized metabolic differences. Furthermore, using high-content image analysis, we monitored NADH responses to PI3K pathway inhibition in hundreds of live cells. As an NADH reporter, Peredox should enable better understanding of bioenergetics.

Imaging Intracellular pH in Live Cells with a Genetically Encoded Red Fluorescent Protein Sensor

Intracellular pH affects protein structure and function, and proton gradients underlie the function of organelles such as lysosomes and mitochondria. We engineered a genetically encoded pH sensor by mutagenesis of the red fluorescent protein mKeima, providing a new tool to image intracellular pH in live cells. This sensor, named pHRed, is the first ratiometric, single-protein red fluorescent sensor of pH. Fluorescence emission of pHRed peaks at 610 nm while exhibiting dual excitation peaks at 440 and 585 nm that can be used for ratiometric imaging. The intensity ratio responds with an apparent pK(a) of 6.6 and a >10-fold dynamic range. Furthermore, pHRed has a pH-responsive fluorescence lifetime that changes by ~0.4 ns over physiological pH values and can be monitored with single-wavelength two-photon excitation. After characterizing the sensor, we tested pHReds ability to monitor intracellular pH by imaging energy-dependent changes in cytosolic and mitochondrial pH.

Quantitative determinants of aerobic glycolysis identify flux through the enzyme GAPDH as a limiting step

Aerobic glycolysis or the Warburg Effect (WE) is characterized by the increased metabolism of glucose to lactate. It remains unknown what quantitative changes to the activity of metabolism are necessary and sufficient for this phenotype. We developed a computational model of glycolysis and an integrated analysis using metabolic control analysis (MCA), metabolomics data, and statistical simulations. We identified and confirmed a novel mode of regulation specific to aerobic glycolysis where flux through GAPDH, the enzyme separating lower and upper glycolysis, is the rate-limiting step in the pathway and the levels of fructose (1,6) bisphosphate (FBP), are predictive of the rate and control points in glycolysis. Strikingly, negative flux control was found and confirmed for several steps thought to be rate-limiting in glycolysis. Together, these findings enumerate the biochemical determinants of the WE and suggest strategies for identifying the contexts in which agents that target glycolysis might be most effective. DOI: http://dx.doi.org/10.7554/eLife.03342.001

Optogenetic reporters: Fluorescent protein-based genetically encoded indicators of signaling and metabolism in the brain.

Fluorescent protein technology has evolved to include genetically encoded biosensors that can monitor levels of ions, metabolites, and enzyme activities as well as protein conformation and even membrane voltage. They are well suited to live-cell microscopy and quantitative analysis, and they can be used in multiple imaging modes, including one- or two-photon fluorescence intensity or lifetime microscopy. Although not nearly complete, there now exists a substantial set of genetically encoded reporters that can be used to monitor many aspects of neuronal and glial biology, and these biosensors can be used to visualize synaptic transmission and activity-dependent signaling in vitro and in vivo. In this review, we present an overview of design strategies for engineering biosensors, including sensor designs using circularly permuted fluorescent proteins and using fluorescence resonance energy transfer between fluorescent proteins. We also provide examples of indicators that sense small ions (e.g., pH, chloride, zinc), metabolites (e.g., glutamate, glucose, ATP, cAMP, lipid metabolites), signaling pathways (e.g., G protein-coupled receptors, Rho GTPases), enzyme activities (e.g., protein kinase A, caspases), and reactive species. We focus on examples where these genetically encoded indicators have been applied to brain-related studies and used with live-cell fluorescence microscopy.

Evaluation of NKX2-2 expression in round cell sarcomas and other tumors with EWSR1 rearrangement: imperfect specificity for Ewing sarcoma.

Ewing sarcoma shows considerable histologic overlap with other round cell tumors. NKX2-2, a homeodomain transcription factor involved in neuroendocrine/glial differentiation and a downstream target of EWSR1-FLI1, has been reported as an immunohistochemical marker for Ewing sarcoma. We assessed the specificity of NKX2-2 for Ewing sarcoma compared with other round cell malignant neoplasms and other soft tissue tumors with EWSR1 translocations. We evaluated whole-tissue sections from 270 cases: 40 Ewing sarcomas (4 with atypical/large cell features), 20 CIC-DUX4 sarcomas, 5 BCOR-CCNB3 sarcomas, 9 unclassified round cell sarcomas, 10 poorly differentiated synovial sarcomas, 10 lymphoblastic lymphomas, 10 alveolar rhabdomyosarcomas, 10 embryonal rhabdomyosarcomas, 10 Merkel cell carcinomas, 10 small cell carcinomas, 20 melanomas, 5 NUT midline carcinomas, 10 Wilms tumors, 10 neuroblastomas, 10 olfactory neuroblastomas, 12 mesenchymal chondrosarcomas, 10 angiomatoid fibrous histiocytomas, 10 clear cell sarcomas, 5 gastrointestinal clear cell sarcoma-like tumors, 5 desmoplastic small round cell tumors, 10 extraskeletal myxoid chondrosarcomas, 10 soft tissue and cutaneous myoepitheliomas, and 19 myoepithelial carcinomas. NKX2-2 positivity was defined as moderate-to-strong nuclear immunoreactivity in at least 5% of cells. NKX2-2 was positive in 37/40 (93%) Ewing sarcomas, including all atypical Ewing sarcomas and cases with known EWSR1-FLI1 or EWSR1-ERG fusion; 85% of Ewing sarcomas showed diffuse (>50%) staining. NKX2-2 was positive in 9 (75%) mesenchymal chondrosarcomas, 8 (80%) olfactory neuroblastomas, 1 CIC-DUX4 sarcoma, 1 poorly differentiated synovial sarcoma, 1 neuroblastoma, 2 unclassified round cell sarcomas, and 3 small cell carcinomas; all other EWSR1-associated tumors were negative for NKX2-2, apart from 1 desmoplastic small round cell tumor, 1 myoepithelioma, and 1 myoepithelial carcinoma. In summary, NKX2-2 is a sensitive but imperfectly specific marker for Ewing sarcoma. Nonetheless, NKX2-2 may be helpful to distinguish Ewing sarcoma from some histologic mimics including CIC-DUX4 and BCOR-CCNB3 sarcomas. Most other EWSR1-associated soft tissue tumors are negative for NKX2-2.

Fosb is a Useful Diagnostic Marker for Pseudomyogenic Hemangioendothelioma

Pseudomyogenic (epithelioid sarcoma-like) hemangioendothelioma is a distinctive vascular neoplasm of intermediate biological potential with a predilection for young adults and frequent multifocal presentation. Pseudomyogenic hemangioendothelioma is characterized by loose fascicles of plump spindled and epithelioid cells with abundant eosinophilic cytoplasm and coexpression of keratins and endothelial markers. Recently, a SERPINE1-FOSB fusion has been identified as a consistent genetic alteration in pseudomyogenic hemangioendothelioma. FOSB gene fusions have also been reported in a subset of epithelioid hemangiomas. The purpose of this study was to assess the potential diagnostic utility of FOSB immunohistochemistry for pseudomyogenic hemangioendothelioma compared with other endothelial neoplasms and histologic mimics. We evaluated whole-tissue sections from 274 cases including 50 pseudomyogenic hemangioendotheliomas, 84 other vascular tumors (24 epithelioid hemangiomas [including 6 cases with angiolymphoid hyperplasia with eosinophilia histology], 20 epithelioid angiosarcomas, 20 epithelioid hemangioendotheliomas [17 CAMTA1 positive, 2 TFE3 positive], 10 spindle-cell angiosarcomas, and 10 epithelioid angiomatous nodules), and 140 other histologic mimics (20 each epithelioid sarcoma, proliferative fasciitis, nodular fasciitis, cellular benign fibrous histiocytoma, spindle-cell squamous cell carcinoma, spindle-cell rhabdomyosarcoma, and leiomyosarcoma). Immunohistochemistry for FOSB was performed following pressure cooker antigen retrieval using a rabbit monoclonal antibody. Diffuse nuclear immunoreactivity for FOSB (>50% of cells) was observed in 48 of 50 (96%) pseudomyogenic hemangioendotheliomas and 13 of 24 (54%) epithelioid hemangiomas (including all angiolymphoid hyperplasia with eosinophilia type). Both FOSB-negative pseudomyogenic hemangioendothelioma cases were decalcified bone tumors. Only 7 other tumors showed diffuse FOSB expression: 2 proliferative fasciitis, 2 nodular fasciitis, 1 epithelioid angiosarcoma, 1 spindle-cell angiosarcoma, and 1 epithelioid hemangioendothelioma. Of note, the FOSB-positive epithelioid hemangioendothelioma was negative for CAMTA1 and TFE3. Focal weak FOSB staining was observed in a subset of histologic mimics and is therefore not diagnostically meaningful. In conclusion, FOSB is a highly sensitive and diagnostically useful marker for pseudomyogenic hemangioendothelioma. Immunohistochemistry for FOSB may be helpful to distinguish pseudomyogenic hemangioendothelioma from histologic mimics including epithelioid sarcoma and other vascular neoplasms. As expected, a subset of epithelioid hemangiomas expresses FOSB, including angiolymphoid hyperplasia with eosinophilia. Although occasional cases of nodular and proliferative fasciitis are positive for FOSB, distinction between these tumor types and pseudomyogenic hemangioendothelioma is usually straightforward based on morphology and other immunophenotypic findings.

A user's guide to non-invasive follicular thyroid neoplasm with papillary-like nuclear features (NIFTP)

The term non‐invasive follicular thyroid neoplasm with papillary‐like nuclear features (NIFTP) was recently introduced to replace a subset of follicular variant of papillary thyroid carcinoma (FVPTC). The goal of this change was to promote more conservative management of these tumours and spare patients the psychological burden of a cancer diagnosis. The histological diagnosis of NIFTP is stringent: the tumour needs to demonstrate encapsulation or circumscription, a purely follicular architecture and the presence of nuclear features of papillary thyroid carcinoma, while lacking capsular and vascular invasion, a significant component of solid growth and high‐grade features (increased mitotic activity and necrosis). In order to ensure that these inclusion and exclusion criteria are met, the tumour must be sampled extensively, with the entire capsule/periphery submitted in all cases. When sampled by fine‐needle aspiration, NIFTP is usually classified within the indeterminate categories of the Bethesda System for Reporting Thyroid Cytopathology. NIFTP is characterized genetically by frequent RAS mutations, although rarely other alterations, such as the BRAF K601E mutation and gene rearrangements in PPARG or THADA, may occur. In this review, we will examine the history of FVPTC and the findings and factors that culminated in the introduction of the NIFTP terminology. A discussion will follow with the histological, cytological and molecular characteristics of NIFTP. We will conclude by considering the potential impact of the introduction of the NIFTP terminology.

Myopericytomatosis: Clinicopathologic Analysis of 11 Cases With Molecular Identification of Recurrent PDGFRB Alterations in Myopericytomatosis and Myopericytoma

Myopericytoma is a benign tumor of concentrically distributed perivascular myoid cells. Its molecular basis and relationship with myofibroma/myofibromatosis and other pericytic tumors are not fully understood. In our consultation/surgical files of over 1000 myopericytic lesions, we identified 11 cases with diffuse dermal/subcutaneous involvement by microscopic myopericytomatous nodules, a phenomenon we have termed myopericytomatosis. Myopericytomatosis affected mostly adults (female:male=8:3; median age, 37 y; range, 9 to 63 y) in the lower extremities (foot/ankle, 5; calf, 3; knee, 1; thigh, 1; neck, 1) over months to 25 years, ranging from 1.5 to 11.0 (median, 6.0) cm in size. Histologically, myopericytomatosis displayed diffuse infiltration by innumerable discrete myopericytoma/myofibroma-like nodules of bland spindled-to-ovoid cells (smooth muscle actin positive), in a mainly perivascular distribution. No mitoses, atypia, or necrosis was noted. All patients were treated by surgical excision (1 patient also received adjuvant radiation), with margins focally positive in 5 of 6 known cases. Of the 6 cases with follow-up of 0.2 to 13.7 (median, 3.4) years, 1 recurred locally twice, while 5 cases showed no recurrence. Targeted next-generation DNA sequencing identified PDGFRB alterations in all cases of myopericytomatosis and conventional myopericytoma tested (5 cases each), including mutations in 4 cases of myopericytomatosis (N666K in 3; Y562-R565 deletion in 1 case) and 3 myopericytomas (Y562C, K653E, and splice acceptor deletion in 1 case each), as well as low-level PDGFRB amplification in 2 cases of myopericytomatosis and 4 myopericytomas. No BRAF, NOTCH, or GLI1 alterations were detected. In summary, myopericytomatosis is a rare, strikingly diffuse, but apparently benign variant of myopericytoma that typically involves superficial soft tissue in adults with innumerable discrete microscopic myopericytomatous nodules. The strongly activating PDGFRB mutation N666K is noted in myopericytomatosis, but not in conventional myopericytoma, suggesting that PDGFRB mutation status may account for their pathogenetic differences. As PDGFRB alterations are present in myopericytoma/myopericytomatosis and infantile myofibromatosis/myofibroma, these entities indeed lie within a histogenetic continuum. Identification of PDGFRB alterations suggests tyrosine kinase inhibition as a potential therapeutic strategy in myopericytic neoplasms if needed.

PHOX2B reliably distinguishes neuroblastoma among small round blue cell tumours

Neuroblastoma shows considerable histological overlap with other small round blue cell tumours. PHOX2B, a transcription factor that is essential for autonomic nervous system development, has been reported as an immunohistochemical marker for neuroblastoma. The aim of this study was to validate the specificity and diagnostic utility of PHOX2B for peripheral neuroblastic tumours.