Deep Profiling of Proteome and Phosphoproteome by Isobaric Labeling, Extensive Liquid Chromatography, and Mass Spectrometry

Mass spectrometry-based proteomics has experienced an unprecedented advance in comprehensive analysis of proteins and posttranslational modifications, with particular technical progress in liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) and isobaric labeling multiplexing capacity. Here, we introduce a deep proteomics profiling protocol that combines 10-plex tandem mass tag (TMT) labeling with an optimized LC-MS/MS platform to quantitate whole proteome and phosphoproteome. The major steps include protein extraction and digestion, TMT labeling, two-dimensional liquid chromatography, TiO₂-mediated phosphopeptide enrichment, high-resolution mass spectrometry, and computational data processing. This protocol routinely leads to confident quantification of more than 10,000 proteins and approximately 30,000 phosphosites in mammalian samples. Quality control steps are implemented for troubleshooting and evaluating experimental variation. Such a multiplexed robust method provides a powerful tool for dissecting proteomic signatures at the systems level in a variety of complex samples, ranging from cell culture, animal tissues to human clinical specimens.

Anxiety, depression and fatigue at 5-year review following CNS demyelination

BACKGROUND

Anxiety and depression are common in multiple sclerosis (MS). We evaluated the prevalence and factors associated with anxiety, depression and fatigue at the 5-year review of a longitudinal cohort study following a first clinical diagnosis of CNS demyelination (FCD).

METHODS

Cases with a FCD were recruited soon after diagnosis and followed annually thereafter. A variety of environmental, behavioural and clinical covariates were measured at five-year review. Anxiety and depression were measured using the Hospital Anxiety & Depression Scale (HADS), and fatigue by the Fatigue Severity Scale (FSS).

RESULTS

Of the 236 cases, 40.2% had clinical anxiety (median HADS-A: 6.0), 16.0% had clinical depression (median HADS-D: 3.0), and 41.3% had clinical fatigue (median FSS: 4.56). The co-occurrence of all three symptoms was 3.76 times greater than expectation. Younger age, higher disability, concussion or other disease diagnosis were independently associated with a higher anxiety score; male sex, higher disability, being unemployed, less physical activity, and antidepressant and/or anxiolytic-sedative medication use were independently associated with a higher depression score. Higher disability, immunomodulatory medication use, other disease diagnosis and anxiolytic-sedative medication use were independently associated with having fatigue, while female sex, higher BMI, having had a concussion, being unemployed and higher disability were associated with a higher fatigue score.

CONCLUSION

These results support previous findings of the commonality of anxiety, depression and fatigue in established MS and extend this to post-FCD and early MS cases. The clustering of the three symptoms indicates that they may share common antecedents.

MicroRNA-26a-interleukin (IL)-6-IL-17 axis regulates the development of non-alcoholic fatty liver disease in a murine model

Non-alcoholic fatty liver disease (NAFLD) is a hepatic presentation of obesity and metabolic syndrome. MicroRNA 26a (Mir-26a) has been reported to play functions in cellular differentiation, cell growth, cell apoptosis and metastasis. A recent paper indicated that Mir-26a regulated insulin sensitivity and metabolism of glucose and lipids. However, the role of Mir-26a in NAFLD still needs to be investigated further. In our current study, vectors encoding pre-Mir-26a (LV-26a) and an empty lentiviral vector (LV-Con) delivered approximately 2 × 10⁷ transforming units of recombinant lentivirus were injected into mice through the tail vein. LV-26a-infected mice were protected from glucose dysmetabolism and showed markedly decreased total liver weight, hepatic triglyceride deposition and serum alanine transaminase (ALT) concentration when compared with LV-Con-treated mice. LV-26a-treated mice also exhibited decreased infiltration of immune cells in the liver - something attributed to reduce infiltration of T cell receptor (TCR)-γδ⁺ , granulocyte-differentiation antigen-1 (Gr-1)⁺ cells and CD11b⁺ cells. Next, we found that Mir-26a inhibited the expression of interleukin (IL)-17 and IL-6 in vivo and in vitro. Furthermore, the decreased expression of IL-17 in the liver tissue induced by Mir-26a was abrogated completely by IL-6 overexpression. The decreased total liver weight, hepatic triglyceride deposition and serum ALT concentration induced by Mir-26a was also abrogated completely by IL-6 over-expression. In conclusion, the Mir-26a-IL-6-IL-17 axis regulates the development of NAFLD in a murine model.

Effect of tofacitinib withdrawal and re-treatment on patient-reported outcomes: results from a Phase 3 study in patients with moderate to severe chronic plaque psoriasis

BACKGROUND

Tofacitinib is an oral Janus kinase inhibitor being investigated for psoriasis. A Phase 3 withdrawal/re-treatment study (NCT01186744; OPT Retreatment) showed tofacitinib re-treatment was effective in patients with chronic plaque psoriasis.

OBJECTIVES

To describe the effects of tofacitinib withdrawal/re-treatment on health-related quality of life (HRQoL) and disease symptoms measured by patient-reported outcomes (PROs).

METHODS

The study was divided into initial treatment, treatment withdrawal, and re-treatment periods. Initial treatment: patients were randomized to receive tofacitinib 5 (n = 331) or 10 mg (n = 335) BID for 24 weeks. Treatment withdrawal: patients who achieved both ≥ 75% reduction in Psoriasis Area and Severity Index (PASI) score from baseline and Physician's Global Assessment of 'clear'/'almost clear' at Week (W)24 received placebo (withdrawal) or the previous dose (continuous treatment). Re-treatment: at relapse (> 50% loss of W24 PASI response) or at W40, patients received their initial tofacitinib dose. PROs included: Dermatology Life Quality Index (DLQI), Itch Severity Item (ISI), Short Form-36 (SF-36) and Patient's Global Assessment (PtGA).

RESULTS

After initial treatment with tofacitinib 5 and 10 mg BID, substantial and significant improvements were reported for mean DLQI (baseline: 12.6 and 12.6; W24: 5.1 and 2.6) and ISI (baseline: 6.7 and 6.9; W24: 2.9 and 1.6). Patients continuously treated with tofacitinib 5 and 10 mg BID maintained those improvements through Week 56 (DLQI: 3.0 and 2.1; ISI: 2.3 and 1.4). By W40, patients withdrawn from tofacitinib 5 and 10 mg BID showed worsening in DLQI (5.0 and 6.2) and ISI (3.7 and 4.0) scores; improvements were regained upon re-treatment (W56, DLQI: 3.4 and 2.4; ISI: 2.2 and 1.6). Similar results were reported for PtGA and SF-36.

CONCLUSION

Continuous tofacitinib treatment provided sustained improvement in HRQoL and disease symptoms. Patients randomized to treatment withdrawal lost initial improvements. Upon re-treatment, improvements were recaptured to levels comparable to those seen with continuous treatment.

Retention of Teeth and Oral Health–Related Quality of Life

The authors aimed to critically review the literature regarding the relationship between retention of teeth and oral health–related quality of life (OHRQoL) and the extent to which tooth retention can ensure OHRQoL among adults. The authors investigated studies that assessed the relationship between number of teeth and OHRQoL and how the position, type, and/or pattern of the teeth is related to OHRQoL. Relevant papers published in English from January 2004 to September 2015 were searched via PubMed and EMBASE. Twenty-nine papers—including cross-sectional, longitudinal, clinical trial, and case-control studies—were included and categorized according to 4 subthemes to achieve the stated aim: 1) number of teeth or missing teeth and OHRQoL, 2) occluding pairs or functional units and OHRQoL, 3) position of remaining or missing teeth and OHRQoL, and 4) shortened dental arches (SDAs) and OHRQoL. The main findings for each subtheme were as follows: 1) A significant association between number of teeth and OHRQoL was shown in most studies; however, those studies found different cutoff points regarding the number of teeth that affect OHRQoL, after adjusting for other factors in the analyses (e.g., age, sex, cultural background, and study locations). 2) The number of occluding pairs and the location of remaining teeth have great impacts on OHRQoL. 3) Having fewer anterior occluding pairs had a greater negative impact on aesthetics and thus affected OHRQoL. 4) Two randomized clinical trials on SDAs indicated that people with SDAs do not show worse OHRQoL than do those with removable dentures. The only 2 population-based studies on SDAs showed that adults with SDAs have no impaired OHRQoL when compared with those having more natural teeth. To conclude, this review found evidence that retention of teeth is associated with better OHRQoL. The number of occluding pairs and the location of remaining teeth have great impacts on OHRQoL. People with SDAs maintain an acceptable level of OHRQoL.

Tofacitinib versus etanercept or placebo in patients with moderate to severe chronic plaque psoriasis: patient-reported outcomes from a Phase 3 study

BACKGROUND

Tofacitinib is an oral Janus kinase inhibitor that is being investigated for psoriasis. Psoriasis impacts on physical and psychological well-being; improvements in health-related quality of life (HRQoL) with etanercept in psoriasis are well documented.

OBJECTIVE

To evaluate HRQoL with tofacitinib, vs. placebo or etanercept, in the Phase 3, randomized, placebo-controlled, non-inferiority, Oral-treatment Psoriasis Trial (OPT) Compare Study (NCT01241591).

METHODS

Adults with moderate to severe chronic plaque psoriasis were randomized 3:3:3:1 to tofacitinib 10 or 5 mg twice daily (BID), etanercept 50 mg twice weekly or placebo, for 12 weeks. Patient-reported outcomes (PROs) included Dermatology Life Quality Index (DLQI), Itch Severity Item and Patient Global Assessment of psoriasis.

RESULTS

At baseline, 83.4% (911/1092) of patients had a DLQI score ranging between 6 and 30, indicating a substantial burden of disease. By Week 12, 47.3%, 43.6% and 30.9% of patients in the tofacitinib 10 mg BID, etanercept and tofacitinib 5 mg BID groups, respectively, had a DLQI score of 0 or 1 (no effect of psoriasis on QoL) vs. 7.8% for placebo (all P < 0.0001). Tofacitinib significantly reduced itch vs. placebo (P < 0.05 both doses) and etanercept (P < 0.0001 both doses) within 1 day of starting treatment. Furthermore, reductions in itch were greater with tofacitinib 10 mg BID, vs. etanercept, at Weeks 2-12 (all time points P < 0.05). At Week 2, an Itch Severity Item score of 'little or no itch' was more frequent with tofacitinib 10 mg (68.6%) vs. etanercept (57.4%) and placebo (12.2%), and the PtGA response rate was significantly greater with tofacitinib 10 mg vs. placebo (P < 0.05).

CONCLUSION

Oral tofacitinib provided significant improvements across multiple PROs by Week 12. Improvements with tofacitinib 10 mg BID were comparable to etanercept, and improvements in itch were greater and more rapid with tofacitinib 10 mg BID.

Guttiferone K impedes cell cycle re-entry of quiescent prostate cancer cells via stabilization of FBXW7 and subsequent c-MYC degradation

Cell cycle re-entry by quiescent cancer cells is an important mechanism for cancer progression. While high levels of c-MYC expression are sufficient for cell cycle re-entry, the modality to block c-MYC expression, and subsequent cell cycle re-entry, is limited. Using reversible quiescence rendered by serum withdrawal or contact inhibition in PTEN(null)/p53(WT) (LNCaP) or PTEN(null)/p53(mut) (PC-3) prostate cancer cells, we have identified a compound that is able to impede cell cycle re-entry through c-MYC. Guttiferone K (GUTK) blocked resumption of DNA synthesis and preserved the cell cycle phase characteristics of quiescent cells after release from the quiescence. In vehicle-treated cells, there was a rapid increase in c-MYC protein levels upon release from the quiescence. However, this increase was inhibited in the presence of GUTK with an associated acceleration in c-MYC protein degradation. The inhibitory effect of GUTK on cell cycle re-entry was significantly reduced in cells overexpressing c-MYC. The protein level of FBXW7, a subunit of E3 ubiquitin ligase responsible for degradation of c-MYC, was reduced upon the release from the quiescence. In contrast, GUTK stabilized FBXW7 protein levels during release from the quiescence. The critical role of FBXW7 was confirmed using siRNA knockdown, which impaired the inhibitory effect of GUTK on c-MYC protein levels and cell cycle re-entry. Administration of GUTK, either in vitro prior to transplantation or in vivo, suppressed the growth of quiescent prostate cancer cell xenografts. Furthermore, elevation of FBXW7 protein levels and reduction of c-MYC protein levels were found in the xenografts of GUTK-treated compared with vehicle-treated mice. Hence, we have identified a compound that is capable of impeding cell cycle re-entry by quiescent PTEN(null)/p53(WT) and PTEN(null)/p53(mut) prostate cancer cells likely by promoting c-MYC protein degradation through stabilization of FBXW7. Its usage as a clinical modality to prevent prostate cancer progression should be further evaluated.

A pilot study of the utility of choline PET-CT in prostate cancer biochemical relapse following radical prostatectomy

INTRODUCTION

To evaluate the detection rate of positive choline PET-CT and its clinical role in assisting with management decisions and the correlation between positive choline PET-CT and clinical/pathological parameters in prostate cancer patients with biochemical relapse following radical prostatectomy.

METHODS

This was a longitudinal observational pilot study of 34 patients who received choline PET-CT scans with biochemical relapse after radical prostatectomy. Variables including peak PSA, PSA doubling time (DT), Gleason score, age, initial PSA at diagnosis, use of ADT prior to PET and initial clinical staging were statistically analysed to assess for independent predictive factors for positive PET findings.

RESULTS

Choline PET-CT was positive in 38.2% of patients (13/34). The only statistically significant predictor for positive PET-CT was the use of ADT prior to PET-CT, with OR 18.7 (95% CI, 2.87-122.45), P < 0.01. Mean peak PSA for patients with positive PET-CT was 5.5 ± 4.8 ng/mL. Patients with positive PET-CT had a mean PSA DT of 5.1 ± 3.8 months and mean total Gleason of 7.6 ± 0.8. Although these variables were not statistically significant, they showed a tendency towards significance. At Receiver Operator Characteristics (ROC) analysis, a peak PSA value of 1.65 ng/mL and PSA DT of 4.4 months were determined to be the optimal cut-off values predicting positive PET-CT.

CONCLUSION

Choline PET-CT has its potential as a diagnostic modality enabling the detection of occult prostate cancer recurrence and to differentiate localised disease from systemic disease thus guiding management. Use of ADT prior to PET-CT is a significant predictor of positive PET-CT. Patients with a short PSA DT, high-peak PSA and high Gleason score should also be considered for choline PET-CT.

[Tissue heterogeneity analysis of CGG-repeat mutation in two fragile X affected male fetuses]

OBJECTIVE

To compare the CGG-repeat-length and its methylation status in fetal tissues and to explicate the heterogeneity of CGG repeats.

METHOD

Multiple tissues from a full mutation(August 2013) and a mosaic aborted fetus of 23-week gestation(May 2012) were collected and genomic DNA from these tissues was extracted. The CGG-repeat-length and methylation status in fetal tissues were determined by a combined strategy of Southern blotting and GC-Rich PCR. FMR1 expression was measured by real time PCR and Western blotting.

RESULT

CGG-repeat-length in different tissues of each fetus was similar.A major methylated band in the full mutation range (540 CGG repeats) was detected in the brain, skin, testis and kidney tissues of Case 1. An unmethylated premutation band with 160 CGG repeats, and another two bands with 470 and 1 100 CGG repeats in the full mutation range were shown in the brain, skin, testis, lung, stomach, gut, liver, kidney, heart and blood of Case 2. However, the methylation status of CGG repeats in the mosaic fetus was heterogeneous among different tissues. The lowest premutation ratio was in the brain of the mosaic fetus compared with other tissues, and correspondingly FMR1 expression in its brain was minimum.

CONCLUSION

This study clarify the tissue heterogeneity of CGG repeats and provides information for the genetic counseling and clinical diagnosis in fragile X syndrome. Based on the fact that the mosaic fetus' mother is a carrier of full mutation, it is speculated that the maternal CGG repeat has contracted before the differentiation of trilaminar germ disc.

Quantitative Susceptibility Mapping in Cerebral Cavernous Malformations: Clinical Correlations

BACKGROUND AND PURPOSE

Quantitative susceptibility mapping has been shown to assess iron content in cerebral cavernous malformations. In this study, our aim was to correlate lesional iron deposition assessed by quantitative susceptibility mapping with clinical and disease features in patients with cerebral cavernous malformations.

MATERIALS AND METHODS

Patients underwent routine clinical scans in addition to quantitative susceptibility mapping on 3T systems. Data from 105 patients met the inclusion criteria. Cerebral cavernous malformation lesions identified on susceptibility maps were cross-verified by T2-weighted images and differentiated on the basis of prior overt hemorrhage. Mean susceptibility per cerebral cavernous malformation lesion (χ̄lesion) was measured to correlate with lesion volume, age at scanning, and hemorrhagic history. Temporal rates of change in χ̄lesion were evaluated in 33 patients.

RESULTS

Average χ̄lesion per patient was positively correlated with patient age at scanning (P < .05, 4.1% change with each decade of life). Cerebral cavernous malformation lesions with prior overt hemorrhages exhibited higher χ̄lesion than those without (P < .05). Changes in χ̄lesion during 3- to 15-month follow-up were small in patients without new hemorrhage between the 2 scans (bias = -0.0003; 95% CI, -0.06-0.06).

CONCLUSIONS

The study revealed a positive correlation between mean quantitative susceptibility mapping signal and patient age in cerebral cavernous malformation lesions, higher mean quantitative susceptibility mapping signal in hemorrhagic lesions, and minimum longitudinal quantitative susceptibility mapping signal change in clinically stable lesions. Quantitative susceptibility mapping has the potential to be a novel imaging biomarker supplementing conventional imaging in cerebral cavernous malformations. The clinical significance of such measures merits further study.

Annual economic burden of hepatitis B virus-related diseases among hospitalized patients in twelve cities in China

A nationwide survey of hepatitis B virus (HBV)-associated economic burden has not previously been performed in China. The purpose of this study was to examine the direct, indirect, and intangible costs of HBV-related diseases within the span of one year. A random sample was taken from specialty and general hospitals across 12 cities in six provinces of China. Intangible costs were estimated based on willingness to pay or open-ended answers provided by patients. The results showed that 27 hospitals were enrolled, with a sample population of 4726 patients (77.7% response rate). The average annual costs were $4454.0 (direct), $924.3 (indirect), and $6611.10 (intangible), corresponding to 37.3%, 7.7%, and 55.1% of the total costs, respectively. The direct medical fees were substantially greater than the non-medical fees. Annual indirect costs were divided into outpatient ($112.9) and inpatient ($811.40) loss of income. The intangible costs of chronic HBV were notably higher than either the direct or indirect costs, consistent with the social stigma in China. The comparison amongst individual cities for the average ratio of direct to indirect costs revealed that the sizes of ratios were negatively correlated with the socioeconomic status of the regions. This study suggested that as a whole in China, the HBV-related diseases caused a heavy financial burden which was positively associated with disease severity. Although the intangible costs coincided with a high prevalence of discrimination against CHB patients in Chinese society, our study may serve as future reference for detailed exploration.

Transitioning from caregiver to visitor in a long-term care facility: the experience of caregivers of people with dementia

OBJECTIVES

Transitioning from the primary caregiver to the visitor in a long-term care facility may be challenging for the caregiver; they are required to surrender their caring duties to the medical and nursing staff. The aim of this study was to explore the experiences of caregivers during their transition from day-to-day caregiver of a person with dementia to a visitor in a long-term care facility.

METHODS

This study utilised a qualitative descriptive design. Twenty caregivers of people with dementia were recruited from the one Aged Rehabilitation and Geriatric Evaluation and Management facility, located in Victoria, Australia. Semi-structured interviews were used to explore the caregiver's experiences. Interviews were analysed using thematic analysis.

RESULTS

The interview data revealed that the participants were undergoing similar experiences. The findings revealed that it was difficult for the caregiver to transition to their new role of visitor; negative reactions of grief, loss of motivation and loneliness were also coupled with positive feelings of relief and the reassurance that their relative or friend would be well cared for and safe within the long-term care facility.

CONCLUSION

The findings offer insight into the experiences felt by caregivers when their relative or friend with dementia is admitted to hospital. Implications of this study include the need to improve the transition process for the caregiver by allowing them to be involved in the decision-making process, keeping them informed of care decisions, and importantly, providing emotional support to help the caregiver positively adapt to this transition.

Effect of oxygen pressure on structure and ionic conductivity of epitaxial Li0.33La0.55TiO3 solid electrolyte thin films produced by pulsed laser deposition

We report on the ionic conductivity of Li_0.33La_0.55TiO₃ (LLTO) epitaxial films grown on the (100) and (111) surfaces of single crystal SrTiO₃ (STO) substrates at different oxygen partial pressures (from 1.33 to 26.66 Pa).

Mapping homeostatic synaptic plasticity using cable properties of dendrites

When chronically silenced, cortical and hippocampal neurons homeostatically upregulate excitatory synaptic function. However, the subcellular position of such changes on the dendritic tree is not clear. We exploited the cable-filtering properties of dendrites to derive a parameter, the dendritic filtering index (DFI), to map the spatial distribution of synaptic currents. Our analysis indicates that young rat cortical neurons globally scale AMPA receptor-mediated currents, while mature hippocampal neurons do not, revealing distinct homeostatic strategies between brain regions and developmental stages. The DFI presents a useful tool for mapping the dendritic origin of synaptic currents and the location of synaptic plasticity changes.