Base-editing mutagenesis maps alleles to tune human T cell functions

CRISPR-enabled screening is a powerful tool for the discovery of genes that control T cell function and has nominated candidate targets for immunotherapies1-6. However, new approaches are required to probe specific nucleotide sequences within key genes. Systematic mutagenesis in primary human T cells could reveal alleles that tune specific phenotypes. DNA base editors are powerful tools for introducing targeted mutations with high efficiency7,8. Here we develop a large-scale base-editing mutagenesis platform with the goal of pinpointing nucleotides that encode amino acid residues that tune primary human T cell activation responses. We generated a library of around 117,000 single guide RNA molecules targeting base editors to protein-coding sites across 385 genes implicated in T cell function and systematically identified protein domains and specific amino acid residues that regulate T cell activation and cytokine production. We found a broad spectrum of alleles with variants encoding critical residues in proteins including PIK3CD, VAV1, LCP2, PLCG1 and DGKZ, including both gain-of-function and loss-of-function mutations. We validated the functional effects of many alleles and further demonstrated that base-editing hits could positively and negatively tune T cell cytotoxic function. Finally, higher-resolution screening using a base editor with relaxed protospacer-adjacent motif requirements9 (NG versus NGG) revealed specific structural domains and protein-protein interaction sites that can be targeted to tune T cell functions. Base-editing screens in primary immune cells thus provide biochemical insights with the potential to accelerate immunotherapy design.

The Tabula Sapiens: A multiple-organ, single-cell transcriptomic atlas of humans

Molecular characterization of cell types using single-cell transcriptome sequencing is revolutionizing cell biology and enabling new insights into the physiology of human organs. We created a human reference atlas comprising nearly 500,000 cells from 24 different tissues and organs, many from the same donor. This atlas enabled molecular characterization of more than 400 cell types, their distribution across tissues, and tissue-specific variation in gene expression. Using multiple tissues from a single donor enabled identification of the clonal distribution of T cells between tissues, identification of the tissue-specific mutation rate in B cells, and analysis of the cell cycle state and proliferative potential of shared cell types across tissues. Cell type-specific RNA splicing was discovered and analyzed across tissues within an individual.

Untargeted lipidomics analysis in women with intrahepatic cholestasis of pregnancy: a cross-sectional study

OBJECTIVE

To compare the plasma lipid profiles in women with normal pregnancies and those with mild or severe intrahepatic cholestasis of pregnancy (ICP). Our goal was to reveal lipidome-wide alterations in ICP and delve into the pathogenesis of ICP from a lipid metabolism perspective.

DESIGN

Cross-sectional study, including women with normal pregnancies, women with mild ICP and women with severe ICP.

SETTING

Gansu Provincial Hospital.

POPULATION

Women with ICP were recruited from October 2019 to March 2020 in Gansu, China.

METHODS

Untargeted lipidomics was used to analyse differentially expressed plasma lipids in controls, in women with mild ICP and in women with severe ICP (n = 30 per group). For lipidomics, liquid chromatography and Q-Exactive Plus Orbitrap mass spectrometry were performed.

MAIN OUTCOME MEASURES

Differentially expressed lipids.

RESULTS

Thirty-three lipids were differentially expressed in the severe and mild ICP groups, compared with the control group, and 20 of those were sphingolipids (ceramide, six species; sphingomyelin, 14 species). All differentially expressed sphingolipids in women with mild ICP were also differentially expressed in women with severe ICP; the fold change and significance of the differential expression were positively correlated with disease severity.

CONCLUSIONS

We systematically characterized the lipidome-wide alterations in mild and severe ICP groups. The results indicated a link between ICP and disordered sphingolipid homeostasis.

TWEETABLE ABSTRACT

Abnormal sphingolipid metabolism is involved in the pathogenesis of ICP.

Targeting C3a/C5a receptors inhibits human mesangial cell proliferation and alleviates immunoglobulin A nephropathy in mice

Complement activation has a deep pathogenic influence in immunoglobulin (Ig)A nephropathy (IgAN). C3a and C5a, small cleavage fragments generated by complement activation, are key mediators of inflammation. The fragments exert broad proinflammatory effects by binding to specific receptors (C3aR and C5aR, respectively). However, no studies thus far have investigated the effects of C3a, C5a and their receptors on IgAN. We observed that C3aR and C5aR antagonists repressed IgA-induced cell proliferation and interleukin (IL)-6 and monocyte chemotactic protein 1 (MCP-1) production in cultured human mesangial cells (HMCs). Furthermore, an IgAN mouse model induced by Sendai virus infection was employed to investigate the effects of C3aR and C5aR on IgAN in vivo for the first time. Wild-type (WT) and several knock-out mouse strains (C3aR^-/- or C5aR^-/- ) were immunized intranasally with increasing doses of inactivated virus for 14 weeks and were subjected to two intravenous viral challenges during the time-period indicated. In the Sendai virus-induced IgAN model, C3aR/C5aR-deficient mice had significantly reduced proteinuria, lower renal IgA and C3 deposition, less histological damage and reduced mesangial proliferation compared with WT mice. Both C3aR deficiency and C5aR deficiency, especially C3aR deficiency, inhibited renal tumour necrosis factor (TNF)-α, transforming growth factor (TGF)-β, IL-1β, IL-6 and MCP-1 expression significantly. However, C3aR/C5aR-deficient and WT mice with IgAN did not differ with respect to their blood urea nitrogen (BUN) and serum creatinine levels. Our findings provide further support for the idea that C3aR and C5aR are crucially important in IgAN, and suggest that pharmaceutically targeting C3aR/C5aR may hold promise for the treatment of IgAN.

High-frequency repetitive transcranial magnetic stimulation over the left DLPFC for major depression: Session-dependent efficacy: A meta-analysis

Background

Depression is a major debilitating psychiatric disorder. Current antidepressant drugs are often associated with side effects or treatment resistance. The aim of this meta-analysis was to evaluate therapeutic effects of high-frequency repetitive transcranial magnetic stimulation (HF-rTMS) in major depression (MD).

Methods

The medical data bases of PubMed, Medline, Embase and Cochrane Central Register were searched for randomized controlled trials (RCTs) reporting the therapeutic effects of high-frequency rTMS for depression, which were published in English between January 1990 and June 2016. The index terms were “depress*”, “depression” and “transcranial magnetic stimulation”. Depression outcome data of different sessions (5, 10, 15, and 20 sessions of rTMS treatment) were extracted and synthesized by calculating standardized mean difference (SMD) with 95% confidence intervals (CI) by using a random-effect model. Within each session group, the subgroup analyses based on the number of pulses (≤ 1000, 1200–1500, 1600–1800, and 2000–3000) were also conducted.

Results

Thirty RCTs with a total of 1754 subjects including 1136 in the rTMS group and 618 in the sham group were included in this meta-analysis. rTMS had a significant overall therapeutic effect on depression severity scores (SMD = −0.73, P < 0.00001). The five, 10, 15, 20 sessions of rTMS treatments yielded the significant mean effect sizes of −0.43, −0.60, −1.13, and −2.74, respectively. In the four groups (5, 10, 15, 20 sessions), the maximal mean effect size was all obtained in the subgroup of 1200–1500 pulses per day (−0.97, −1.14, −1.91, −5.47; P < 0.05).

Conclusions

The increasing of HF-rTMS sessions is associated with the increased efficacy of HF-rTMS in reducing depressed patients’ symptom severity. A total number of pulses of 1200–1500 per day appear to deliver the best antidepressant effects of HF-rTMS.

Effects of soybean resistance on variability in life history traits of the higher trophic level parasitoid Meteorus pulchricornis (Hymenoptera: Braconidae)

To extrapolate the influence of plant cultivars varying in resistance levels to hosts on parasitoid life history traits, we estimated variation in parasitoid developmental and reproductive performances as a function of resistance in soybean cultivars, which were randomly chosen from a line of resistant genotypes. Our study showed that the parasitoid Meteorus pulchricornis varied widely in offspring survival and lifetime fecundity, but varied slightly in development time and adult body size, in response to the soybean cultivars that varied in resistance to the host Spodoptera litura. Furthermore, the variability in survival and lifetime fecundity was different between attacking the 2nd and the 4th instar host larvae, varying more in survival but less in lifetime fecundity when attacking the 4th than 2nd instar larvae. Our study provides further evidence supporting that plant resistance to herbivorous hosts have variable effects on different life history traits of higher trophic level parasitoids.

Cation exchange synthesis of uniform PbSe/PbS core/shell tetra-pods and their use as near-infrared photodetectors

In this work we explore the preparation of complex-shaped semiconductor nanostructures composed of different materials via a cationic exchange process in which the cations of the original semiconductor nanostructure are replaced by cations of different metals with preservation of the shape and the anionic framework of the nanocrystals. Utilizing this cation exchange method, we synthesized two new tetrapods for the first time: Cu2-xSe/Cu2-xS and PbSe/PbS, both prepared from CdSe/CdS tetrapods as 'templates'. We also fabricated near-infrared (NIR) photodetectors with a very simple architecture comprising a PbSe/PbS tetrapod layer between two Au electrodes on a glass substrate. When illuminated by a NIR laser, these devices are capable of achieving a responsivity of 11.9 A W(-1) without the use of ligand-exchange processes, thermal annealing or hybrid device architecture. Transient absorption spectroscopy was carried out on these PbSe/PbS tetrapods, the results of which suggest that the branched morphology contributes in part to device performance. Investigation of the charge dynamics of the PbSe/PbS tetrapods revealed an extremely long-lived exciton recombination lifetime of ∼17 ms, which can result in enhanced photoconductive gain. Overall, these heterostructured tetrapods showcase simultaneously the importance of nanoparticle shape, band structure, and surface chemistry in the attainment of NIR photodetection.

Parallel Epidemics of Community-Associated Methicillin-Resistant Staphylococcus aureus USA300 Infection in North and South America

BACKGROUND

The community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) epidemic in the United States is attributed to the spread of the USA300 clone. An epidemic of CA-MRSA closely related to USA300 has occurred in northern South America (USA300 Latin-American variant, USA300-LV). Using phylogenomic analysis, we aimed to understand the relationships between these 2 epidemics.

METHODS

We sequenced the genomes of 51 MRSA clinical isolates collected between 1999 and 2012 from the United States, Colombia, Venezuela, and Ecuador. Phylogenetic analysis was used to infer the relationships and times since the divergence of the major clades.

RESULTS

Phylogenetic analyses revealed 2 dominant clades that segregated by geographical region, had a putative common ancestor in 1975, and originated in 1989, in North America, and in 1985, in South America. Emergence of these parallel epidemics coincides with the independent acquisition of the arginine catabolic mobile element (ACME) in North American isolates and a novel copper and mercury resistance (COMER) mobile element in South American isolates.

CONCLUSIONS

Our results reveal the existence of 2 parallel USA300 epidemics that shared a recent common ancestor. The simultaneous rapid dissemination of these 2 epidemic clades suggests the presence of shared, potentially convergent adaptations that enhance fitness and ability to spread.

Transferable vancomycin resistance in a community-associated MRSA lineage

We report the case of a patient from Brazil with a bloodstream infection caused by a strain of methicillin-resistant Staphylococcus aureus (MRSA) that was susceptible to vancomycin (designated BR-VSSA) but that acquired the vanA gene cluster during antibiotic therapy and became resistant to vancomycin (designated BR-VRSA). Both strains belong to the sequence type (ST) 8 community-associated genetic lineage that carries the staphylococcal chromosomal cassette mec (SCCmec) type IVa and the S. aureus protein A gene (spa) type t292 and are phylogenetically related to MRSA lineage USA300. A conjugative plasmid of 55,706 bp (pBRZ01) carrying the vanA cluster was identified and readily transferred to other staphylococci. The pBRZ01 plasmid harbors DNA sequences that are typical of the plasmid-associated replication genes rep24 or rep21 described in community-associated MRSA strains from Australia (pWBG745). The presence and dissemination of community-associated MRSA containing vanA could become a serious public health concern.

The Effect of Temperature on the Deformation of Diamond Surfaces

A brief review is given of recently published work on the fracture and plastic flow of natural and synthetic diamond crystals when deformed by softer impressors at elevated temperatures. Under these conditions, a brittle-ductile transition (BDT) temperature for the different types of diamond has been established.

In this paper we show that below the BDT temperature, brittle ‘chatter’ cracking on {111} cleavage planes accounts for anisotropic wear provided that the mean contact pressure exceeds about 10 GPa. Above the BDT temperature, titanium diboride sliders develop contact pressures sufficient to cause extensive plastic deformation of the diamond specimens but insufficient to produce cleavage fracture. However, repeated sliding with TiB2 does lead to cumulative plastic flow preceding fatigue type fracture on {110} planes. Using cubic boron nitride and diamond sliders above the BD T temperature leads to a combination of both plastic deformation and {110} cracking. The coefficient offriction is a maximum in <100> and a minimum in <110> directions. and the measured scratch hardness, which confirms that the <100> directions are softer than <110>, is shown to be consistent with the predictions of a resolved shear stress model which was de velopedffor explaining anisotropy in all crystals.

Abstract PD07-02: βIII Tubulin Expression by Immunohistochemistry (IHC) and mRNA in a Randomized Phase 2 Neoadjuvant Breast Cancer (BC) Study of Ixabepilone (ixa) Compared to Paclitaxel (pac)

Background: Overexpression of βIII tubulin has been shown to correlate with poor prognosis and reduced response to taxanes. Ixa exhibits activity in βIII overexpressing tumor models and BC patients (pts) with high βIII mRNA levels. We report the prevalence of βIII by a validated IHC assay and the correlation of βIII protein and mRNA expression in BC tissue samples. Methods: In this neoadjuvant BC study CA163-100, 295 patients were randomized 1:1 to ixa (40 mg/m2 IV x 4 cycles) or pac (80 mg/m2 IV wkly x 12) after all pts received 4 cycles of doxorubicin (60 mg/m2) plus cyclophosphamide (600 mg/m2). Pre-chemotherapy formalin-fixed paraffin-embedded pt tissue sections were assessed for intensity and percentage of tumor cell staining of βIII by IHC. RNA was extracted from additional pre-chemotherapy core needle biopsy specimens and profiled for gene expression using Affymetrix HG-U133Av2 gene chips. Tumors were classified as basal-like, Her2-enriched, luminal-like A and B and normal-like using a 50-gene subtype predictor. In addition, Her2 and hormone receptor status was used for tumor subtyping. Results: βIII staining data were obtained for 261 pts, of which 247 were randomized to either ixa or pac arms of study CA163-100. The prevalence of βIII positivity was 39.1% (102/261) using the prespecified cut-off of ≥50% (2+, 3+) positive cells. The distribution of IHC scores was bimodal. 64% of specimens classified as βIII negative had no observable staining, while 77% of βIII positive specimens had a majority of tumor cells staining at the highest intensity (3+). IHC and gene expression profiling data were available for 235 pts and a correlation between βIII tubulin protein and mRNA expression was observed. The relative βIII mRNA expression levels were significantly higher in pts classified as βIII positive vs. βIII negative by IHC (P&lt;0.0001) and 80% of tumors classified as βIII tubulin positive by IHC, had high relative TUBB3 mRNA levels, using a median cut-off. An association between βIII IHC status and breast cancer subtypes was also seen with 69% (62/90) of βIII positive specimens also classified as basal-like and conversely, 55% (62/113) of basal-likes classified as βIII positive. Nearly half (48%) the specimens in this cohort were basal-like, a classification that was quite concordant with triple negative status and as such, triple negative tumors were also enriched for βIII positivity. Conclusion: βIII is reliably measured by a validated IHC assay, providing a bimodal distribution of scores in this BC study. Correlative analyses of βIII status by BC subtype suggest that βIII positivity is significantly associated with aggressive basal-like/TN breast cancers. The clinical utility of βIII as a potential tool to select patients who may benefit from ixa in this study will be presented separately.

Citation Information: Cancer Res 2010;70(24 Suppl):Abstract nr PD07-02.

Abstract PD07-01: Phase 2 Study of Ixabepilone Versus Paclitaxel as Neoadjuvant Therapy for Early Stage Breast Cancer with Comparative Biomarker Analysis

Background: Anthracyclines (A) and taxanes (T) are standard neoadjuvant treatments for breast cancer (BC), achieving pathologic complete response (pCR) rates of 20-30% in unselected patient (pt) populations. Ixabepilone (ixa) is approved for treatment of metastatic BC: plus capecitabine (Cap) in pts progressing after A and T or as monotherapy after progression on A, T and Cap. Prior data suggest that overexpression of βIII tubulin is associated with resistance to paclitaxel (P) while activity of ixa was unaffected. We present the first randomized comparison of neoadjuvant ixa and P in early stage BC. Primary objectives were to estimate pathologic complete response rate (pCR) in the overall population and in biomarker-defined populations. Methods Pts with early stage BC were biopsied for immunohistochemical (IHC) and mRNA biomarker analyses prior to chemotherapy. Following 4 cycles of doxorubicin/cyclophosphamide (AC), pts were randomized to either every 3 week ixa (40mg/m2:4 cycles) or weekly P (80mg/m2:12 doses). Post-therapy surgery and pathological reports were used to assess pCR. Baseline βIII expression was assessed via a standardized IHC assay (Dako, CA) and predefined single gene mRNA markers (including TUBB3, CAPG, TACC3) were assessed via Affymetrix gene expression profilling. The pCR rate and cutoff for biomarker positivity were estimated using a cross-validation method. Secondary endpoints in the study included clinical objective response rate and safety. Results Pts (N=384) were enrolled in 15 countries: 313 pts were treated with AC. 295 pts were randomized; 289 were treated with either ixa or P. Of these, 247 (123, ixa; 124, P) had βIII IHC data and 231 (114, ixa; 117, P) had both pathologic and βIII IHC data. Baseline characteristics were balanced between arms, including triple negative pts (TN, 49%). The pCR rate in all randomized pts was 24.3% (90% CI: 18.6-30.8) with ixa and 25.2% (90% CI: 19.4-31.7) with P. pCR rates were similar regardless of sub-group.

Table 1. pCR rates

No significant interaction was observed between βIII expression and treatment arms (logistic regression analysis). Secondary efficacy measures were consistent with the pCR results. No clinically meaningful differences in efficacy endpoints were noted between ixa and P with mRNA markers (TUBB3, CAPG and TACC3; analyses are ongoing with others). The safety profiles of ixa and P were similar, including incidence of peripheral neuropathy (Grade 3/4: ixa 4.1% vs P 3.5%). An exception was greater neutropenia with ixa (Grade 3/4; 41.3% versus 8.4% with P) although there was no difference in the rate of febrile neutropenia (0.7%). Summary Overall, the results indicated that ixa had similar efficacy to P when measured by pCR in the neoadjuvant BC setting. No clinically meaningful differences were noted in the efficacy profile of ixa compared to P across the subsets analyzed. Ixa or P following AC was well tolerated with similar safety profiles.

Development of rapid immunoassays for the detection of ractopamine in swine urine

The monoclonal antibodies (mAbs) against ractopamine (Rac) were prepared and their properties identified by indirect competitive enzyme-linked immunoabsorbant assay (ELISA). The IC(50) of mAbs was 2.7 ng ml(-1) towards Rac or 9.3 ng ml(-1) towards Rac-glucuronides and no cross-reactivity (CR) towards other competitors except dobutamine (CR: 3.76%). Based on the mAbs, the Rac-kit (kit) and Rac-strip (strip) were developed to detect Rac residues in swine urine. The strip and kit assay could be performed within 5-10 min and 2 h, respectively, allowing the analysis of urine samples without the need for sample clean-up. The detection limits were 1 ng ml(-1) for kit and 3 ng ml(-1) with the unaided eye, and 0.2 ng ml(-1) with the Strip Reader for strip. The correlation coefficients (R(2)) were 0.988 for kit in the range 0-128.0 ng ml(-1), and 0.987 for strip in the range 0-10.8 ng ml(-1). Comparing the gas chromatography-mass spectrometry (GC-MS) with the kit or strip in swine urine spiked with Rac standards, the differences ranged from 1.4% to 4.5% for kit and 1.0% to 4.7% for strip. However, the differences were greater than 54% for the kit and 55% for the strip test for the analysis of urine from swine treated with Rac. The results obtained from GC-MS using hydrolysed urine samples were generally in good agreement with those obtained from strip or kit using non-hydrolysed urine samples.

Thyroid cancer in pregnancy

OBJECTIVE

To compare stage at diagnosis, treatment and survival among pregnant women with thyroid cancer to non-pregnant women with thyroid cancer, and to assess the impact of treatment on maternal and perinatal outcomes.

METHODS

A database containing maternal and newborn discharge records linked to the California Cancer Registry was queried to obtain information on all thyroid cancers from 1991-1999. Women with thyroid cancer occurring during pregnancy were compared to age-matched non-pregnant women with thyroid cancer.

RESULTS

595 cases of thyroid cancers were identified (129 antepartum and 466 postpartum). About 64% of thyroid cancers were diagnosed at stage 2 among pregnant women versus 58% among non-pregnant controls. The odds of thyroid cancer were 1.5 times higher among Asian/Pacific Islanders than among Non-Hispanic White women. Pregnancy had no significant effect on mortality after diagnosis of thyroid cancer. Thyroidectomy during pregnancy was not associated with adverse maternal or neonatal outcomes.

CONCLUSIONS

Thyroid cancer discovered during or after pregnancy does not appear to have a significant impact on the prognosis of the disease.

The effects of isolation rearing on glutamate receptor NMDAR1A mRNA expression determined by in situ hybridization in Fawn hooded and Wistar rats

Rats reared in social isolation exhibit a syndrome of behavioral and biochemical effects indicative of enhanced mesolimbic dopamine (DA) function. The precise nature of the neurodevelopmental changes that produce this state are unknown but result in enhanced DA neurotransmission in the nucleus accumbens (NAC). It was hypothesized that this may be the indirect result of chronic changes in glutamate NMDA receptor function. The same prediction has been made for Fawn hooded (FH) rats that exhibit some of the characteristic effects of isolation-reared rats when compared to Wistar rats. Therefore, mRNA levels of the NMDAR1A receptor subunit were determined by in situ hybridization and were quantified in the striatum, hippocampus and prefrontal cortex of FH and Wistar rats. Isolation rearing alone was not found to have an effect on the expression of NMDAR1A, while FH rats had reduced levels across most brain regions examined. In some areas of the striatum and prefrontal cortex, this effect was greater in FH isolates than in FH socials, while in the hippocampus, the opposite was observed.

Developmental vulnerabilities to the onset and course of bipolar disorder

Different types of psychosocial stressors have long been recognized as potential precipitants of both unipolar and bipolar affective episodes and the causative agents in posttraumatic stress disorder (PTSD). New preclinical data have revealed some of the neurobiological mechanisms that could convey the long-term behavioral and biochemical consequences of early stressors. Depending on the timing, quality, quantity, and degree of repetition, maternal deprivation stress in the neonatal rodent can be associated with lifelong anxiety-like behaviors, increases in stress hormones and peptides. and proneness to drug and alcohol administration, in association with acute changes in the rate of neurogenesis and apoptosis (preprogrammed cell death) and decrements in neurotrophic factors and signal transduction enzymes necessary for learning and memory. Patients with bipolar illness who have a history of early extreme adversity (physical or sexual abuse in childhood or adolescence), compared with those without, show an earlier onset of illness, faster cycling frequencies, increased suicidality, more Axis I and Axis II comorbidities (including alcohol and substance abuse), and more time ill in more than 2 years of prospective follow-up. These findings are subject to a variety of interpretations, but to the extent that the more severe course of bipolar illness characteristics are directly and causally related to these early stressful experiences, early recognition and treatment of high-risk children could be crucial in helping to prevent or ameliorate the long-term adverse consequences of these stressors.

Hepatopoietin acts as an autocrine growth factor in hepatoma cells

Hepatopoietin (HPO) is a novel human hepatotrophic factor. Its known function is mainly limited to supporting liver regeneration. Recently, it was shown by our laboratory that HPO acts as a mitogen for hepatoma cell lines and that there are HPO-specific receptors on the surface of these cells (Wang, G., et al., J Biol Chem 1999;274:11469-11472), indicating that HPO might be involved in oncogenesis in the liver. To study this hypothesis, we first conducted experiments in vitro to identify the existence of an autocrine loop of HPO/HPO receptor in hepatoma cell lines. It was demonstrated that HPO was actually expressed by hepatoma cells, such as HepG2, Bel 7402, and SMMC-7721, and secreted into the culture medium. Furthermore, it was shown that HPO-neutralizing antibody has an inhibitory effect on the uptake of tritiated thymidine by hepatoma cells. The results strongly suggest that HPO acts as an autocrine factor for hepatoma cells in vitro.

[A preliminary study of a hearing screening model for newborn]

OBJECTIVE

To search for a hearing screening model for newborn and to investigate the prevalence of newborn hearing loss in our country.

METHODS

The distortion product otoacoustic emissions (DPOAE) was used to test the hearing in 2,998 of 3,075 newborns before discharge. Otoacoustic emissions (OAE) was again used for cases failed in the hospital screening 4 weeks later. Those cases failed in both screening steps were finally tested by auditory brainstem response (ABR). All infants failed in ABR test received diagnostic evaluation audiologically to identify the category and degree of hearing loss. The pass criterion of DPOAE was defined as signal-noise-ratio (SNR) exceeding 6 dB in 4 of 5 frequencies between 1.5-6 kHz. The pass criterion of ABR was the presence of wave V in response to 35 dB nHL click stimuli.

RESULTS

The OAE screening in the hospital showed that 2,710 (90.4%) newborns passed the first test. Two hundred and sixty three of 288 newborns passed the second OAE screening after one month. Six of 25 infants failed in ABR test were eventually identified to be hearing impaired.

CONCLUSION

Two-stages screening, combining OAE and ABR tests, may be an ideal model for newborn hearing screening. The prevalence of congenital hearing loss is similar to that reported in the literature.

Proteomic analysis of apoptosis initiation induced by all-trans retinoic acid in human acute promyelocytic leukemia cells

The irreversible destiny of apoptosis in its early stage might play a critical role in the apoptosis of human acute promyelocytic leukemia (APL) cell line induced by all-trans retinoic acid (ATRA). To characterize protein alterations during the apoptosis-initiation phase and to understand the metabolic status at that time, we investigated the protein profiles in the apoptosis-initiation phase of APL cell line HL-60 by proteomic analysis. ATRA-withdrawal was conducted to demonstrate that there was committed initiation phase of apoptosis triggered by 10(-6) M ATRA at day 3. Only after that time point, ATRA-treated cells irreversibly went to apoptosis. Also at that time point, the positive regulators of apoptosis such as STAT3 increased at protein level, whereas negative regulators (Bcl-2 and p-STAT3) decreased. In addition, caspase-3 also increased after that time. Furthermore, comparative proteomic analysis was utilized to examine the protein expression profiles during the initiation stage of apoptosis. Our results showed 12 upregulated and 7 downregulated proteins experiencing twofold alteration, including key regulators of signal transduction such as G-proteins and nucleic receptors, proteins related with metabolism, oxidation and reduction, proteins associated with the nucleus and cytoskeleton-related proteins. Some of them could be positive modulators to trigger apoptosis, whereas others could contribute to intracellular defense against apoptosis induced by exogenous triggers. The results above suggest that there is a subtle balance between apoptosis and the intracellular defense against apoptosis. Once the balance is disturbed, cells would irreversibly initiate to undergo the execution of apoptosis.

Gene expression profiling in human fetal liver and identification of tissue- and developmental-stage-specific genes through compiled expression profiles and efficient cloning of full-length cDNAs

Fetal liver intriguingly consists of hepatic parenchymal cells and hematopoietic stem/progenitor cells. Human fetal liver aged 22 wk of gestation (HFL22w) corresponds to the turning point between immigration and emigration of the hematopoietic system. To gain further molecular insight into its developmental and functional characteristics, HFL22w was studied by generating expressed sequence tags (ESTs) and by analyzing the compiled expression profiles of liver at different developmental stages. A total of 13,077 ESTs were sequenced from a 3'-directed cDNA library of HFL22w, and classified as follows: 5819 (44.5%) matched to known genes; 5460 (41.8%) exhibited no significant homology to known genes; and the remaining 1798 (13.7%) were genomic sequences of unknown function, mitochondrial genomic sequences, or repetitive sequences. Integration of ESTs of known human genes generated a profile including 1660 genes that could be divided into 15 gene categories according to their functions. Genes related to general housekeeping, ESTs associated with hematopoiesis, and liver-specific genes were highly expressed. Genes for signal transduction and those associated with diseases, abnormalities, or transcription regulation were also noticeably active. By comparing the expression profiles, we identified six gene groups that were associated with different developmental stages of human fetal liver, tumorigenesis, different physiological functions of Itoh cells against the other types of hepatic cells, and fetal hematopoiesis. The gene expression profile therefore reflected the unique functional characteristics of HFL22w remarkably. Meanwhile, 110 full-length cDNAs of novel genes were cloned and sequenced. These novel genes might contribute to our understanding of the unique functional characteristics of the human fetal liver at 22 wk.

[Characteristics of N2O emissions from vegetal soils on Fildes peninsula, Antarctica]

The N2O fluxes from the vegetal soils were first measured on the Fildes peninsula, Antarctica, and the total N2O emission was also estimated in the summer 2 months. The daily variations of N2O fluxes appeared single-peak trend under the sunshine or rainy weather conditions but they were irregular under the snow weather conditions and inconsistent with the atmospheric temperatures. The seasonal variations of the N2O fluxes were affected by the temperature and rainfall. The conditions during the transitions between dry and wet seasons improved the N2O emission. The total N2O emissions from moss and lichen soils were 3.7152 kg and 2.5344 kg, respectively. It follows that the vegetal soils are the sources for the atmospheric N2O on the Fildes peninsula, Antarctica.

Kainate receptor-mediated heterosynaptic facilitation in the amygdala

Prolonged low-frequency stimulation of excitatory afferents to basolateral amygdala neurons results in enduring enhancement of excitatory synaptic responses. The induction of this form of synaptic plasticity is eliminated by selective antagonists of GluR5 kainate receptors and can be mimicked by the GluR5 agonist ATPA. Kainate receptor-mediated synaptic facilitation generalizes to include inactive afferent synapses on the target neurons, and therefore contrasts with other types of activity-dependent enduring synaptic facilitation that are input-pathway specific. Such heterosynaptic spread of synaptic facilitation could account for adaptive and pathological expansion in the set of critical internal and external stimuli that trigger amygdala-dependent behavioral responses.

Increased sensitivity to seizures in repeated exposures to hyperbaric oxygen: role of NOS activation

Nitric oxide is involved in the mechanism of hyperbaric oxygen (HBO(2)) brain toxicity as nitric oxide synthase (NOS) inhibitors delay latent time before the onset of seizures. The purpose of this study was to investigate if seizures affect sensitivity to convulsions during subsequent exposure to HBO(2) and to determine if NOS activity and expression is changed after HBO(2) seizures. Rats were exposed to 5 atm (gauge pressure) 100% O(2) until seizures recorded by electroencephalograph (EEG) and reexposed 1, 2, or 6 days later. Latency to seizures was significantly shorter (P<0.05) in animals reexposed 1 or 2 days after the first exposure. Activity of calcium-dependent NOS activity in cortex was significantly higher 1 and 2 days after seizures compared with controls (P<0.05), while calcium-independent NOS activity was not changed during the 6-day post-seizure interval. The expression of neuronal NOS (nNOS) protein determined by Western blot was higher 1 and 2 days after seizures (P<0.05), while the expression of endothelial (eNOS) and inducible (iNOS) remained unchanged. nNOS upregulation 1 and 2 days after seizures and protection against HBO(2) seizures by nNOS-specific inhibitor 7-nitroindazole (7-NI) suggest possible involvement of NO in the mechanism of increased sensitivity to HBO(2) in reexposures.

cDNA transfection of amino-terminal fragment of urokinase efficiently inhibits cancer cell invasion and metastasis

Focusing of urokinase-type plasminogen activator (uPA) to the cell surface via binding to its specific receptor (uPAR, CD87) is critical for tumor invasion and metastasis. Consequently, the inhibition of uPA-uPAR interaction on the cell surface might be a promising anti-invasion and anti-metastasis strategy. We examined the effects of cDNA transfection of the human uPA amino-terminal fragment (ATF) on invasion and metastasis of cancer cells. First, a highly metastatic human lung giant-cell carcinoma cell line (PG), used as the target cell for evaluation of this effect, was demonstrated to express both uPA and uPAR. Then, ATF, which contains an intact uPAR binding site but is catalytically inactive, was designed as an antagonist of uPA-uPAR interaction and was transfected into PG cells. [(3)H]-Thymidine incorporation and cell growth curves indicated that expressed ATF did not affect the proliferation of transfected cells. However, analysis by scanning electron microscopy revealed that ATF changed the host cells from the typical invasive phenotype to a noninvasive one. Correspondingly, the modified Boyden chamber test in vitro showed that ATF expression significantly decreased the invasive capacity of transfected cells. Furthermore, in the spontaneous metastasis model, it was confirmed in vivo that expressed ATF remarkably inhibited lung metastasis of implanted ATF-transfected PG cells. In summary, autocrine ATF could act as an antagonist of uPA-uPAR interaction, and ATF cDNA transfection could efficiently inhibit the invasion and metastasis of the cancer cells. Inhibition of uPA-uPAR interaction on the cell surface might be a promising anti-invasion and anti-metastasis strategy.

Designing metal-peptide models for protein structure and function

Recent progress in the rational design of metal sites within peptide model systems shows increasing control in the placement of metals within helical bundles and inclusion of sophisticated elements such as second-sphere ligand interactions. A crystallographically characterized two-metal peptide model for diiron proteins represents a major achievement in de novo design methodologies. Increasingly complex and robust models for electron transfer through and between helices, and electrode-supported electron-transfer peptides, have been constructed. Design elements for peptide-supported ferredoxins and mononuclear Fe(II) and Zn(II) sites have been refined.

[Experimental study of anti-metastasis effect of urokinase amino-terminal fragment gene on human breast cancer cells]

OBJECTIVE

To explore the suppressive effects of urokinase amino-terminal fragment (ATF) gene on metastatic potential of human breast cancer cell line MCF-7.

METHODS

A pcDNA3-ATF plasmid containing ATF cDNA under CMV promotor/enhancer control was constructed and transfected into MCF-7 cells by lipofectin. The expression of of uPA/uPAR and ATF in MCF-7 cells were analyzed by RT-PCR and Western blot. The effect of ATF expression on invasiveness in vitro, tumorigenesis and metastasis in vivo of MCF-7 cell was investigated.

RESULTS

MCF-7 cells displayed an overexpression of uPA/uPAR. Expression of ATF was detected after ATF gene-transfection. The invasive capacity of ATF gene-transfected MCF-7 cells was decreased significantly. Although the tumorigenesis was not affected, the in vivo metastasis of ATF gene-transfected MCF-7 cells was remarkably inhibited.

CONCLUSION

Suppression of invasiveness and metastasis of ATF-transfected MCF-7 cells is perhaps due to a competitive inhibition of interaction with endogenous uPA/uPAR.

Functional characterization of novel human ARFGAP3

ADP ribosylation factors (ARFs) are critical in the vesicular trafficking pathway. ARF activity is controlled by GTPase-activating proteins (GAPs). We have identified recently a novel tentative ARF GAP derived from human fetal liver, ARFGAP3 (originally named as ARFGAP1). In the present study, we demonstrated that ARFGAP3 had GAP activity in vitro and remarked that the GAP activity of ARFGAP3 was regulated by phospholipids, i.e. phosphatidylinositol 4,5-diphosphate as agonist and phosphatidylcholine as antagonist. ARFGAP3 is a predominantly cytosolic protein, and concentrated in the perinuclear region. Its transient ectopic overexpression in cultured mammalian cells reduced the constitutive secretion of secreted alkaline phosphatase, indicating that ectopic overexpression of ARFGAP3 inhibits the early secretory pathway of proteins in vivo. These results demonstrated that ARFGAP3 is a novel GAP for ARF1 and might be involved in intracellular traffic of proteins and vesicular transport as predicted.

Characterization and tissue expression of a novel human gene npdc1

We report the molecular characterization of a novel human homologue of mouse npdc1 (neural proliferation, differentiation and control, 1) gene, designated human npdc1 (hnpdc1). hnpdc1 was identified by large-scale sequencing of fetal liver cDNA libraries and the full-length cDNA was obtained by PCR amplification. The hnpdc1 gene, which contains nine exons, was mapped to human chromosome 15. It encodes a polypeptide of 325 amino acids, which shows high homology (77% identity) to the mouse NPDC1. Sequence analysis has shown that hNPDC1 protein contains a putative signal peptide of 34 amino acids, a transmembrane segment, and a typical bipartite nuclear localization signal. Northern blot and dot blot hybridization indicates that, just like mnpdc1, hnpdc1 mRNA is strongly expressed in adult brain (especially in hippocampus, frontal lobe and temporal lobe) and about 1.82-fold higher in adult brain than that in fetal brain. Unlike mnpdc1, however, hnpdc1 contains two transcripts instead of only one (1.5 kb), and has high expression levels in prostate, pituitary gland, and mammary glands. These results support that hNPDC1 plays a role in the control of neural cell proliferation and differentiation, and suggest that it may be involved in the development of several secretion glands.

[Diagnosis and treatment of horizontal canal benign paroxysmal positional vertigo]

OBJECTIVE

To explore effective methods for the diagnosis and treatment of horizontal-canal benign paroxysmal positional vertigo (HC-BPPV).

METHODS

Medical records from nine patients with HC-BPPV, treated between July 1996 and March 2000, were retrospectively analyzed. Data of complete history, audiograms, positional tests and neuro-otological examinations were collected. All patients were treated with a particle repositioning maneuver called the "barbecue rotation" which starts with the patient in the supine position and consists of three 90-degree head rotations towards the unaffected ear.

RESULTS

HC-BPPV was characterized by brief attacks of intense vertigo that were induced mainly by rolling over in bed (9/9) and turning the head to either side while upright (5/9). In most cases, rotation to the pathological side from supine position caused a very intense horizontal nystagmus beating towards the undermost ear. Findings such as latency and fatigability, which are common features of posterior-canal BPPV (PC-BPPV), were not present. After the barbecue rotation, all patients had immediate and sustained relief of their attacks during the 4 to 15 months' follow up.

CONCLUSION

HC-BPPV is different from PC-BPPV and other vertiginous diseases in typical presentations and positional testing results. The barbecue rotation is a successful method for curing the disorder.

Water stress and accumulation of beta-N-oxalyl-L-alpha,beta-diaminopropionic acid in grass pea (Lathyrus sativus)

Grass pea seedlings were grown in an irrigated field. Roots of 15-day-old seedlings were treated with PEG, and leaves were studied. With the duration of PEG treatment, changes in the lipid peroxidation and activities of superoxide dismutase, catalase, peroxidase, and glutathione reductase as well as contents of hydrogen peroxide and beta-N-oxalyl-L-alpha,beta-diaminopropionic acid (ODAP) were assayed. The results indicate that with the duration of PEG treatment, activities of superoxide dismutase, peroxidase, and catalase decreased, whereas contents of hydrogen peroxide and ODAP, extent of lipid peroxidation, and activity of glutathione reductase increased. Both diethyldithiocarbamate and aminotriazole strongly inhibit activities of superoxide dismutase and catalase, respectively. At same time, the extent of lipid peroxidation was obviously increased. However, mannitol decreased the extent of lipid peroxidation. Diethyldithiocarbamate, aminotriazole, and mannitol do not affect the accumulation of ODAP. The observations suggest that there is no direct relationship between the accumulation of ODAP and the metabolism of free radicals. In addition, the relationship between water stress and ODAP accumulation in grass pea is discussed.

Stimulation of the mitogen-activated protein kinase cascade and tyrosine phosphorylation of the epidermal growth factor receptor by hepatopoietin

Hepatopoietin (HPO) is a novel human hepatotrophic growth factor, which specifically stimulates proliferation of cultured primary hepatocytes in vitro and liver regeneration after liver partial hepatectomy in vivo. Recently, the identification of the mitogenic effect of HPO on hepatoma cell lines and the existence of HPO-specific receptors indicate that HPO acts via its specific cell surface receptor. However, the molecular mechanism of HPO action is not fully elucidated. In this report, we examined the signal transduction events induced by HPO in hepatoma cell line (HepG2). Our results demonstrated that HPO induces phosphorylation of mitogen-activated protein kinase kinase and mitogen-activated protein kinase (MAPK) in a rapid and transient manner. HPO stimulates tyrosine phosphorylation of epidermal growth factor receptor (EGFR). Furthermore, we observed that both MAPK activation and the mitogenic effect of HPO on HepG2 cells were completely blocked by AG1478, a specific inhibitor of EGFR tyrosine kinase activity. However, the effects of HPO were not antagonized by an EGFR-blocking antibody, mAb528, which blocks the interaction between epidermal growth factor and EGFR, indicating that stimulation of tyrosine phosphorylation of EGFR by HPO was not mediated by epidermal growth factor. In contrast, genistein, a general tyrosine kinase inhibitor, significantly attenuated the tyrosine phosphorylation of EGFR in response to HPO. In conclusion, our results suggest that tyrosine phosphorylation of EGFR may play a critical role in MAPK activation and mitogenic stimulation by HPO.

[Whole genome-wide scanning for a large pedigree with matrilineal deafness]

OBJECTIVE

To search responsible nuclear genes for matrilineal non-syndromic deafness.

METHODS

Whole genome-wide scanning was performed to analyze the 365 short tandem repeats in a deaf pedigree with maternal inheritance using DNA pooling strategy. Frequencies of allele in one patient pool were compared with that in one unaffected relative pool as well as in one normal control pool. Linkage analysis was also conducted in some positive loci.

RESULTS

Allele from 45 loci occurred more frequently in the patient pool than that in the unaffected relative pool and the control pool. No linkage was found from any candidate locus investigated.

CONCLUSION

45 positive loci obtained from this family may be as the candidate positions for matrilineal non-syndromic deafness.

[Accumulation of ABA and ODAP in Lathyrus sativus under water stress]

The roots of fifteen days old Lathyrus sativus seedlings were treated by PEG, PEG + ABA and ABA, and their leaves were sampled to determine the contents of endogenic ABA, ODAP, MDA and H2O2 and the activity of superoxide dismutase, catalase, peroxidase and glutathione reductase. The results showed that after treated, the contents of ABA and ODAP in leaves increased markedly. The addition of exogenous ABA decreased the increment of MDA and H2O2 contents and retarded the attenuation of CAT activity, which were induced by PEG stress, and enhanced the GR activity. In addition, when materials were treated with exogenous ABA in a long time, the ABA content in leaves was increased markedly, and ODAP was then accumulated. There was no significant effect on metabolism of active oxygen in the early days(0-3 days) of ABA treatment, but the activities of SOD, POD, CAT and GR decreased, and the contents of MDA and H2O2 increased in leaves of Lathyrus sativus with the duration of ABA treatment(7-15 days). The results indicated that ABA could promote the accumulation of ODAP in leaves of Lathyrus sativus.

[Audiological findings and mitochondrial DNA mutation in a large family with matrilineal sensorineural hearing loss]

OBJECTIVE

To explore audiological features of matrilineal non-syndromic deafness and its molecular mechanism.

METHODS

A large family with 41 members having inherited deafness was studied. Complete history and the data of general and otolaryngological examinations were collected. All subjects were screened for mitochondrial DNA A1555G mutation by molecular analysis. Audiological evaluation included puretone audiometry, auditory brainstem responses and transiently evoked otoacoustic emissions.

RESULTS

All subjects were in good health generally. Molecular analysis showed that all maternal relatives with or without hearing loss harbored the A1555G mitochondrial mutation. No mutation was found among spouses and paternal relatives. Audiological results showed notable symmetric bilateral sensorineural hearing loss in 17 of 20 maternal relatives, in which 5 cases had a progressive hearing loss in the recent 11 years. The age of appearance of hearing loss ranged from 1 to 50 years.

CONCLUSION

All hearing-impaired subjects of this family had late-onset sensorineural hearing loss. Most of which were progressive. The A1555G mitochondrial mutation in the 12S rRNA gene is responsible for the disorder. Other factors, such as nuclear genes or environmental determinants, may influence the clinical expression of mutant mtDNA.

Characterization, chromosomal assignment, and tissue expression of a novel human gene belonging to the ARF GAP family

We have identified and characterized a novel human ADP-ribosylation factor GTPase-activating protein (ARFGAP1) gene that is related to other members of the ARF GAP family. The full-length cDNA for human ARFGAP1 was cloned following the identification of an EST obtained by large-scale cDNA library sequencing through a Blast search of public databases. Structurally, ARFGAP1 encodes a polypeptide of 516 amino acids, which contained a typical GATA-1-type zinc finger motif (CXXCX(16)CXXC) with the four cysteine residues that are highly conserved among other members of the ARF GAP family. The conserved ARF GAP domain may emphasize the biological importance of this gene. The ARFGAP1 gene, which contained 16 exons ranging from 0.5 to 9.3 kb, was mapped to human chromosome 22q13.2-q13.3 using radiation hybridization and in silico analyses. ARFGAP1 is strongly expressed in endocrine glands and testis. Interestingly, the expression of ARFGAP1 in testis is about sixfold higher than that in ovary, indicating a possible role of ARFGAP1 in the physiological function of sperm. Expression of ARFGAP1 in four human fetal tissues and seven cancer cell lines was also detected.