SWEET: a single-sample network inference method for deciphering individual features in disease

Recently, extracting inherent biological system information (e.g. cellular networks) from genome-wide expression profiles for developing personalized diagnostic and therapeutic strategies has become increasingly important. However, accurately constructing single-sample networks (SINs) to capture individual characteristics and heterogeneity in disease remains challenging. Here, we propose a sample-specific-weighted correlation network (SWEET) method to model SINs by integrating the genome-wide sample-to-sample correlation (i.e. sample weights) with the differential network between perturbed and aggregate networks. For a group of samples, the genome-wide sample weights can be assessed without prior knowledge of intrinsic subpopulations to address the network edge number bias caused by sample size differences. Compared with the state-of-the-art SIN inference methods, the SWEET SINs in 16 cancers more likely fit the scale-free property, display higher overlap with the human interactomes and perform better in identifying three types of cancer-related genes. Moreover, integrating SWEET SINs with a network proximity measure facilitates characterizing individual features and therapy in diseases, such as somatic mutation, mut-driver and essential genes. Biological experiments further validated two candidate repurposable drugs, albendazole for head and neck squamous cell carcinoma (HNSCC) and lung adenocarcinoma (LUAD) and encorafenib for HNSCC. By applying SWEET, we also identified two possible LUAD subtypes that exhibit distinct clinical features and molecular mechanisms. Overall, the SWEET method complements current SIN inference and analysis methods and presents a view of biological systems at the network level to offer numerous clues for further investigation and clinical translation in network medicine and precision medicine.

Prevalence of the Taiwan variant of the Epstein-Barr virus in nasopharyngeal carcinoma patients and normal individuals

BACKGROUND

Latent membrane protein 1 (LMP1) of Epstein-Barr virus (EBV) is a potentially oncogenic protein, able to inhibit differentiation and induce transformation of epithelial cells. The LMP1 gene sequence of EBV in nasopharyngeal carcinoma (NPC) differs from that of EBV in B95-8 cells. A change of nucleotide at the XhoI site results in loss of the restriction site in the EBV LMP1 gene from NPC, and this of EBV is designated as the Taiwan variant. In this study, we further investigated the Taiwan variant of EBV in nasopharyngeal biopsies and throat washings of NPC patients and normal controls.

METHODS

DNA was extracted from nasopharyngeal biopsies of 22 NPC patients and 40 normal controls, and from throat washings of 28 NPC patients and 78 normal controls. The DNA was amplified by polymerase chain reaction (PCR) using LMP1 gene-specific primers, then the EBV variant was identified by analysis with the XhoI restriction enzyme.

RESULTS

The LMP1 gene was detected in all NPC tumors, in only 25 of 40 normal nasopharyngeal biopsies, and in 12 of 28 and 44 of 78, respectively, throat washings of NPC patients and normal controls. The Taiwan variant was detected in 84.1% to 100% of EBV isolates. The distribution of Taiwan variant EBV was not statistically different between the NPC group and normal controls in either nasopharyngeal biopsies or throat washings.

CONCLUSIONS

The results indicate that, based on XhoI restriction site analysis, the Taiwan variant of EBV is the predominant EBV strain in NPC patients and normal individuals in Taiwan.

Expression of IsK protein mRNA in cultured rat strial marginal cells

A cell culture system of marginal cells (MC) of the rat stria vascularis was established by the explant method. When grown on plastic dishes, cultured MC showed a polygonal "cobblestone-like" appearance. Dome formation, composed of several hundreds to thousands of cells, occurring after confluence suggested that vectorial transport of ion(s) with accompanying fluid developed in the cultured MC. Transmission electron microscopy demonstrated junctional complexes formed of tight junctions and desmosomes at the upper lateral membranes. The polymerase chain reaction (PCR) product, amplified with primers made from the cDNA reverse transcribed from cultured MC, yielded a distinct band compatible with the expected size of the PCR products amplified from cDNA of positive control groups containing IsK protein, indicating that cultured MC expressed the IsK protein mRNA. The results show that cultured MC can form large domes and express the most characteristic IsK protein, indicating that they maintain their vectorial electrolyte transport function and, possibly, the ability to secrete K+ in this condition.

Detection of IgA against Epstein-Barr virus BZLF-1 replication activator (ZEBRA) in sera of nasopharyngeal carcinoma patients with a recombinant ZEBRA protein

BACKGROUND

Epstein-Barr virus (EBV) is closely associated with nasopharyngeal carcinoma (NPC). An EBV-encoded immediate-early antigen, BZLF-1 replication activator (ZEBRA) initiates EBV replication and expression in all NPC tumors. In this study, we investigated whether immunoglobulin A (IgA) against ZEBRA is present in the sera of patients with NPC, and whether it was able to be determined by enzyme-linked immunosorbent assay (ELISA) using a recombinant ZEBRA prepared from Escherichia coli.

METHODS

A polymerase chain reaction-amplified cDNA fragment of the ZEBRA gene was inserted into the expression vector of E coli under the control of an IpL promoter. E coli bacteria containing the CI857 gene served as host to overexpress the ZEBRA protein by heat induction. Recombinant ZEBRA was collected by mechanical disruption of the bacteria, purified by column chromatography, and analyzed by SDS-PAGE and Western blot assay using sera from NPC patients. The recombinant ZEBRA was used to develop the ELISA to detect IgA against ZEBRA.

RESULTS

The amount of ZEBRA produced comprised 30% of total E coli protein. Western blot assay confirmed that affinity of the recombinant ZEBRA to IgA antibody was preserved. IgA against ZEBRA was shown to be positive by ELISA in 36 of 40 NPC sera, but in only nine of 55 patients with other head and neck malignancies, and two of 35 normal individuals. For serologic diagnosis of NPC, the sensitivity of IgA/ZEBRA detected by ELISA was 90% and the specificity was 87.4%.

CONCLUSIONS

A recombinant ZEBRA was produced at high levels in E coli and retained affinity to IgA against ZEBRA. The recombinant ZEBRA was successfully used to develop an ELISA for the detection of IgA against ZEBRA. The high sensitivity and specificity of IgA against ZEBRA show that the ELISA is feasible for serologic diagnosis of NPC.

Malignant otitis externa

BACKGROUND

Malignant otitis externa is an infrequent but severe infection of the external auditory canal, most often affecting elderly diabetic patients. Early diagnosis is necessary due to its high morbidity and mortality.

METHODS

From 1990 to 1997, all patients with malignant otitis externa at the Veterans General Hospital-Taipei were reviewed retrospectively. The clinical features and the strategy of diagnosis and treatment are discussed.

RESULTS

Twelve patients with an average age of 65.3 years were included. Eleven of these patients were diabetic. All had the presenting symptoms of otalgia and otorrhea at diagnosis. Bacterial cultures grew Pseudomonas aeruginosa in eight patients and methicillin-resistant Staphylococcus aureus in four patients. The mean duration of admission was 82 days. Appropriate antibiotics were given according to the results of bacterial culture and sensitivity test. 99Technetium scans and 67gallium scans were performed to evaluate the extent of involvement and monitor the effects of treatment. Eventually, four patients died due to renal failure, meningitis, pneumonia and upper gastrointestinal bleeding, respectively.

CONCLUSIONS

Malignant otitis externa is a life-threatening infection arising from the external auditory canal. A high degree of suspicion for malignant otitis externa is mandatory. Vigorous local and systemic antimicrobial treatment should be initiated early in the course of the disease to achieve a satisfactory outcome. 99Technetium and 67gallium scans are important for the diagnosis and evaluation of the treatment results.

cAMP mediates transepithelial K+ and Na+ transport in a strial marginal cell line

Because cytoplasmic cAMP has been reported to be the secondary messenger mediating K+ transport in marginal cells of freshly isolated stria vascularis, the possible role of cAMP in ion transport processes of an immortalized marginal cell line (MCPV-8) showing evidence of K+ and Na+ reabsorption was evaluated in this study. Confluent MCPV-8 monolayers were mounted into Ussing chambers and perfused on both sides with perilymph-like Ringer's solution. Transepithelial short-circuit current (I(SC)), resistance (R(T)) and open-circuit voltage (V(T)) were measured using voltage clamp technique. The following results were obtained. (1) Addition of forskolin (10(-4) M) to the basolateral perfusate increased I(SC) to 311 +/- 42%; no significant change in RT was observed. Addition of BaCl2 (2 mM) to the apical perfusate at the maximal response of forskolin blocked 50-60% of I(SC) and subsequent addition of amiloride (10(-5) M) to the apical perfusate further blocked I(SC) to a value close to 0. (2) To evaluate the effect of cellular cAMP on Ba2+-sensitive K+ current, amiloride-sensitive Na+ current was blocked first by addition of amiloride (10(-5) M) to the apical perfusate; subsequent addition of 3-isobutyl-1-methylxanthine (IBMX, 1 mM) or N6,2'-O-dibutyryladenosine 3',5'-cyclic monophosphate (dbcAMP, 1 mM) to the basolateral perfusate increased I(SC) to 175 +/- 13 and 411 +/- 32%, respectively. The stimulated I(SC) was blocked to close to 0 by addition of BaCl2 (2 mM) to the apical perfusate. N2,2'-O-Dibutyrylguanosine 3',5'-cyclic monophosphate (dbcGMP, 1 mM) had no effect on I(SC). (3) To assess the effect of cellular cAMP on amiloride-sensitive Na+ current, Ba2+-sensitive K+ current was blocked in advance by addition of BaCl2 to the apical perfusate; subsequent addition of IBMX or dbcAMP to the basolateral perfusate increased I(SC) to 219 +/- 21% and 388 +/- 39%, respectively. The stimulated I(SC) was blocked to close to 0 by addition of amiloride to the apical perfusate. dbcGMP had no effect on I(SC). Hence, these results suggest that cellular cAMP is the secondary messenger that mediates the transepithelial transport of both K+ and Na+ in MCPV-8 monolayers.

Effects of acute brainstem compression on auditory brainstem response in the guinea pig

BACKGROUND

The purpose of this study was to establish the norm for parameters of auditory brainstem response (ABR) in the guinea pig and to investigate if acute brainstem compression results in significant changes to these parameters.

METHODS

Thirty-six guinea pigs with positive Preyer's reflex were anesthetized. A craniectomy was performed to remove the right occipital bone and the dura mater was opened to expose the brain, cerebellum and cerebellopontine angle (CPA). A small inflatable balloon was placed into the CPA precisely and slowly. ABR was recorded before incision of the skin as a baseline value, after placement and after inflation of the balloon with water at 0.1-ml intervals.

RESULTS

Five stable peaks were recorded in 27 experimental animals. When the balloon was inflated with 0.1 ml water, the absolute latency (AL) of peaks IV and V and the interpeak latency (IPL) of peaks III and IV, and IV and V were prolonged. The amplitude ratios (AR) of peaks II, III, IV and V to peak I decreased. Inflation of the balloon with 0.2 ml of water caused further elongation of ALs of peaks IV and V and decreases in each AR. When the balloon volume increased to 0.3 ml, peak V became unrecognizable and peaks III and IV showed significant elongation of AL; peaks I and II did not show significant change in ALs. Further increase of the balloon volume to 0.4 ml resulted in disappearance of peaks III, IV and V; AL of peak II was also elongated. However, the amplitude and AL of peak I remained unchanged. Similar changes were observed in IPLs.

CONCLUSIONS

This study establishes the norm of parameters of ABR in guinea pigs and demonstrates that acute brainstem compression causes elongation of ALs and IPLs of peaks II, III, IV and V. This suggests that peaks II, III, IV and V come from the brainstem and that peak I is not generated from the brainstem in the guinea pig.

Establishment and characterization of a strial marginal cell line maintaining vectorial electrolyte transport

E6/E7 genes of human papilloma virus type 16 were used to immortalize a primary culture of marginal cells (MC) from gerbils. One of the cloned lines was selected which demonstrated preservation of the main characteristics of the MC, both morphologically and physiologically. Electron microscopic examination showed well-developed junctional complexes and apical microvilli which suggested its epithelial origin. Polymerase chain reaction (PCR) demonstrated the incorporation of E6/E7 genes with the genome. Reverse transcription PCR revealed the existence of mRNA of the IsK channel, a unique marker of MC among the inner ear cells, in this clone. Flow cytometric analysis of this cell line's DNA content was diploid. Numerous large domes formed after confluence of the cell monolayer. Electrophysiologic studies displayed evidence of apical K+ and Na+ channels which were blocked by Ba2+ (2 mM) and amiloride (10(-5) M), respectively. Existence of basolateral Na,K-ATPase and Na+/Cl-/K+ cotransporter was shown by blockage by ouabain (10(-3) M) and bumetanide (50 microM), individually. Injection of the cell line to nude mice failed to induce growth of tumors. This cell line was serum-, density- and anchorage-dependent when cultured in plastic dishes. In conclusion, this cell line shows characteristics of well-differentiated MC maintaining the major ionic transport processes, and provides us a good model to study the possible mechanisms and regulating factors of endolymph production.

Oxygen metabolites modulate sodium transport in gerbil middle ear epithelium: involvement of PGE2

The middle ear epithelium and respiratory epithelia share basic properties such as homeostasis of air-filled cavities and mucociliary clearance toward the pharynx. With the middle ear SV40-transformed (MESV) cell line, we used the short-circuit current (Isc) technique to investigate changes in ion transport induced by oxidants. Xanthine and xanthine oxidase on the basal side of the monolayers dramatically increased Isc up to 50%. This effect was not affected by superoxide dismutase or mannitol, but could be blunted by catalase or 1,3-dimethyl-2-thiourea. Increasing concentrations of H2O2 from 10(-5) to 5 x 10(-4) M produced a dose-dependent increase in Isc from 0.26 +/- 0.16 up to 4.21 +/- 0.43 microA/cm2 (P < 0.05, n = 5). Concentration of half-maximal stimulation (EC50) was 4.68 x 10(-5) M. This effect was inhibited by indomethacin and was related to a sodium transport, since the H2O2-induced increase in Isc could be prevented or abolished by 1) apical addition of benzamil (10(-6)M) and 2) substitution of sodium with N-methyl-glucamine. H2O2 exposure also induced indomethacin-sensitive increase in released prostaglandin (PG) E2 (EC50 = 5.62 x 10(-5) M) and in cAMP content (EC50 = 3.95 x 10(-5) M) with similar kinetics. These results suggest that exposure of MESV cells to oxidants stimulates the production of PGE2, which in turn increases the transepithelial sodium transport rate.

Stimulation of sodium transport by oxidants in middle ear epithelium in primary culture

Primary cultures of middle ear (ME) epithelial cells from gerbils were used to investigate the effect on ion transport of reactive oxygen species (ROS), which are major inflammatory mediators. Short-circuit current measurements revealed an unexpected result: low concentrations of ROS induced an increase in transepithelial sodium transport. This stimulation was mediated by the endogenous synthesis of prostaglandin E2, which in turn increased the intracellular adenosine 3',5'-cyclic monophosphate (cAMP) content. This effect was blunted by indomethacin. By stimulating sodium and fluid transport, ROS may reduce the depth of the periciliary fluid layer, and may thus be involved in the impairment of mucociliary clearance which initiates chronic otitis media.

Modulation of cyclic AMP production by strial marginal cells from gerbil in culture

To further investigate the role of marginal cells (MCs) in the secretion of endolymph and because of the limitations encountered in investigating these cells in vivo, we used primary cultures of MCs derived from explants of gerbil stria vascularis and investigated modulation of the adenylate cyclase-cyclic AMP system. After 10 days on type I collagen coated plastic dishes, a confluent monolayer of epithelial-like cells was obtained which exhibited the morphologic and immunohistochemical features of the native marginal cells. The cyclic AMP (cAMP) content was determined at 37 degrees C, after 5 min of incubation with various agents, in the presence of a specific inhibitor of type III cAMP-dependent phosphodiesterase, RO 20-1724. The adenylate cyclase-cAMP system was associated with beta 2-adrenergic receptors. The cAMP content was increased by isoproterenol (23-fold), a beta-agonist, but not by octopamine, an alpha-agonist, and the affinity for ICI 118.551, a specific beta 2-antagonist, was greater than for CGP 20712A, a specific beta 1-antagonist (Kd: 0.03 x 10(-6) M and 15 x 10(-6) M respectively). The cAMP content was maximally increased by prostaglandin E2 > beta 2-adrenergic agonist >> vasopressine type 2 receptor agonist (26-, 23-, and 3-fold the basal cAMP content, respectively). The present study demonstrates that cultured marginal cells retain some of their in vivo properties including a modulated enzymatic cAMP system. This culture model should allow further in-depth investigation of the function of marginal cells.

Pathophysiology of middle ear epithelium: a new role for prostaglandin E2

INTRODUCTION

Otitis media with effusion is a disease of the middle ear epithelium resulting from a decreased sol layer as well as increased mucus secretion and plasma-derived protein transudation, which causes mucus plugging. Because the epithelium keeps the middle ear cavities fluid-free and air-filled, we investigated its fluid transport capacities, which may be involved in both efficacy of the mucociliary clearance and drying-out of the posterior ear cavities (Yen PT et al: Acta Otolaryngol (Stockh) 113, 1993). We have established the absorptive capacity of middle ear epithelial cells in primary culture (Herman P, et al: Am J Physiol 262, 1992). However, the paucity of cells obtained by enzymatic digestion led us to develop a new model for further investigation of middle ear epithelial cell.

METHODS

We established a middle ear cell line (MESV) using simian virus 40 (SV40) infection of middle ear epithelial cells from the Mongolian gerbil.

RESULTS

Investigation of the transport processes using the short-circuit current technique showed that MESV cells retain most characteristics of the original middle ear epithelial cells. Transepithelial sodium transport from the apical to the basal side was responsible for the transepithelial lumen-negative potential difference.

CONCLUSION

The presence of high concentrations of prostaglandin E2 in the middle ear effusions has been documented. This work investigates the effect of prostaglandin E2 on the rate of transepithelial ion transport of MESV cells. Prostaglandin E2 increased the rate of electrogenic sodium transport by means of increase in the intracellular cyclic adenosine monophosphate (cAMP) content. Such a modulation of sodium transport in the course of otitis media could be responsible for the reduced periciliary sol layer that impairs the mucociliary clearance.

[Ventilation tube insertion for treating adult otitis media with effusion]

The etiologic factors and treatment of otitis media with effusion (OME) in children are well described and established. On the contrary, little has been published with regard to OME in adults and its treatment. To further investigate this problem, we reviewed the records of all adult patients who had received ventilation tube (VT) insertion for OME in VGH-Taipei from 1983 to 1986. There were 335 VT insertions performed on 140 adult patients whose follow-up periods were longer than 6 months. Among them, fifty patients received more than one VT insertion due to recurrence of OME in one or both ears. The average follow-up period was more than 4 years. The coexistence of nasal diseases was found in 46% of the adult OME patients. The mean extrusion time of the VT was 10.2 months. After VT insertions, the improvements of mean air conduction and mean air-bone conduction gap were 10.1 and 11.8 dB respectively. After the extrusion or removal of VT, there was no recurrence of OME in 50 ears (14.9%). Recurrence of OME occurred in 199 ears (59.4%). Dry persistent perforations of the eardrums were found in 27 ears (8.1%). Discharging persistent perforations were noted in 24 ears (7.2%). No recurrence of OME was observed in 24.2% of the ears with serous effusion fluids, whereas only 4.8% of the ears with mucoid fluids were free from recurrence during the follow-up period. Post-intubation otorrhea, which was the most common complication, developed in 92 ears (27.5%). Our results suggest that the recurrence rate of OME after extrusion of VT is high in the adult patients.(ABSTRACT TRUNCATED AT 250 WORDS)