DPHL: A DIA Pan-human Protein Mass Spectrometry Library for Robust Biomarker Discovery

To address the increasing need for detecting and validating protein biomarkers in clinical specimens, mass spectrometry (MS)-based targeted proteomic techniques, including the selected reaction monitoring (SRM), parallel reaction monitoring (PRM), and massively parallel data-independent acquisition (DIA), have been developed. For optimal performance, they require the fragment ion spectra of targeted peptides as prior knowledge. In this report, we describe a MS pipeline and spectral resource to support targeted proteomics studies for human tissue samples. To build the spectral resource, we integrated common open-source MS computational tools to assemble a freely accessible computational workflow based on Docker. We then applied the workflow to generate DPHL, a comprehensive DIA pan-human library, from 1096 data-dependent acquisition (DDA) MS raw files for 16 types of cancer samples. This extensive spectral resource was then applied to a proteomic study of 17 prostate cancer (PCa) patients. Thereafter, PRM validation was applied to a larger study of 57 PCa patients and the differential expression of three proteins in prostate tumor was validated. As a second application, the DPHL spectral resource was applied to a study consisting of plasma samples from 19 diffuse large B cell lymphoma (DLBCL) patients and 18 healthy control subjects. Differentially expressed proteins between DLBCL patients and healthy control subjects were detected by DIA-MS and confirmed by PRM. These data demonstrate that the DPHL supports DIA and PRM MS pipelines for robust protein biomarker discovery. DPHL is freely accessible at https://www.iprox.org/page/project.html?id=IPX0001400000

Predominantly night-time feeding and weight outcomes in infants

Background: The influence of circadian feeding patterns on weight outcomes has been demonstrated in animal and human studies but not in very young children. Objective: We aimed to examine the association of infant circadian feeding patterns at 12 months with subsequent growth and weight status after one year. Design: Mothers from a Singapore birth cohort (n=349) reported food given to their infant and the feeding time at 12 months of age. Predominantly day-time (pDT, 0700-1859h, n=282) and predominantly night-time (pNT, 1900-0659h, n=67) feeding infants were defined by whether daytime energy intake was &gt;50% or &lt;50% of total energy intake assessed by 24-hour recall. Body Mass Index Z-scores (BAZ) were computed using World Health Organization Child Growth Standards 2006 to determine changes in BAZ from 12 to 24 months and weight status at 24 months. Multivariable linear and logistic regression analyses were performed.Results: Compared to pDT feeding, pNT feeding was associated with higher BAZ gain from 12-24 months (adjusted ?=0.38, 95% CI=0.11 to 0.65, p=0.006) and an increased risk of becoming overweight at 24 months (adjusted OR=2.78, 95% CI=1.11 to 6.97, p=0.029), with adjustments for maternal age, education, ethnicity, monthly household income, parity, infant BAZ at 12 months, feeding mode in the first six months of life and total daily energy intake.Conclusion: Our study suggests that the role of daily distribution of energy consumption in weight regulation begins in infancy. Feeding infants predominantly during night-time hours was associated with adiposity gain and risk of overweight in early childhood. Including advice on appropriate feeding time may be considered when implementing strategies to combat childhood obesity. <br/

Downstream E-Box–mediated Regulation of the Human Telomerase Reverse Transcriptase (hTERT) Gene Transcription: Evidence for an Endogenous Mechanism of Transcriptional Repression

Regulation of the hTERT gene encoding the telomerase catalytic subunit plays an important role in human cell senescence, immortalization, and carcinogenesis. By examining the activity of various deleted or mutated hTERT promoter fragments, we show that an E-box element downstream of the transcription initiation site is critical to differential hTERT transcription between the telomerase/hTERT-positive renal cell carcinoma cell line (RCC23) and its telomerase/hTERT-negative counterpart containing a transferred, normal chromosome 3 (RCC23+3). This E-box element mediated repression of hTERT transcription in RCC23+3 but not in RCC23. A copy number–dependent enhancement of the repression suggested active repression, rather than loss of activation, in RCC23+3. Endogenous expression levels of c-Myc or Mad1, which could activate or repress hTERT transcription when overexpressed, did not account for the differential hTERT transcription. Gel mobility shift assays identified the upstream stimulatory factors (USFs) as a major E-box–binding protein complex in both RCC23 and RCC23+3 and, importantly, detected an RCC23+3-specific, E-box–binding factor that was distinct from the USF and Myc/Mad families. The E-box–mediated repression was also active in normal human fibroblasts and epithelial cells and inactive in some, but not all, telomerase/hTERT-positive cancer cells. These findings provide evidence for an endogenous, repressive mechanism that actively functions in telomerase/hTERT-negative normal cells and becomes defective during carcinogenic processes, e.g., by an inactivation of the telomerase repressor gene on chromosome 3