In vivo mRNA display enables large-scale proteomics by next generation sequencing

Multimodal Omics Approaches to Aging and Age-Related Diseases

Aging is associated with a progressive decline in physiological capacities and an increased risk of aging-associated disorders. An increasing body of experimental evidence shows that aging is a complex biological process coordinately regulated by multiple factors at different molecular layers. Thus, it is difficult to delineate the overall systematic aging changes based on single-layer data. Instead, multimodal omics approaches, in which data are acquired and analyzed using complementary omics technologies, such as genomics, transcriptomics, and epigenomics, are needed for gaining insights into the precise molecular regulatory mechanisms that trigger aging. In recent years, multimodal omics sequencing technologies that can reveal complex regulatory networks and specific phenotypic changes have been developed and widely applied to decode aging and age-related diseases. This review summarizes the classification and progress of multimodal omics approaches, as well as the rapidly growing number of articles reporting on their application in the field of aging research, and outlines new developments in the clinical treatment of age-related diseases based on omics technologies.

HGF secreted by hUC-MSCs mitigates neuronal apoptosis to repair the injured spinal cord via phosphorylation of Akt/FoxO3a pathway

Spinal cord injury (SCI) can cause severe and permanent neurological damage, and neuronal apoptosis could inhibit functional recovery of damaged spinal cord greatly. Human umbilical cord mesenchymal stem cells (hUC-MSCs) have great potential to repair SCI because of a series of advantages, including inhibition of neuronal apoptosis and multiple differentiation. The former may play an important role. However, the detailed regulatory mechanism associated with the inhibition of neuronal apoptosis after hUC-MSCs administration has not been elucidated. In this study, proteomics analysis of precious human cerebrospinal fluid (CSF) samples collected from SCI subjects receiving hUC-MSCs delivery indicated that hepatocyte growth factor (HGF) is largely involved in SCI repair. Furthermore, overexpression of HGF derived from hUC-MSCs could decrease reactive oxygen species to prevent neuron apoptosis to the maximum, and thus lead to significant recovery of spinal cord dysfunction. Moreover, HGF could promote phosphorylation of Akt/FoxO3a pathway to decrease reactive oxygen species to reduce neuron apoptosis. For the first time, our research revealed that HGF secreted by hUC-MSCs inhibits neuron apoptosis by phosphorylation of Akt/FoxO3a to repair SCI. This study provides important clues associated with drug selection for the effective treatment of SCI in humans.

De Novo Single-Stranded RNA-Binding Peptides Discovered by Codon-Restricted mRNA Display

RNA-binding proteins participate in diverse cellular processes, including DNA repair, post-transcriptional modification, and cancer progression through their interactions with RNAs, making them attractive for biotechnological applications. While nature provides an array of naturally occurring RNA-binding proteins, developing de novo RNA-binding peptides remains challenging. In particular, tailoring peptides to target single-stranded RNA with low complexity is difficult due to the inherent structural flexibility of RNA molecules. Here, we developed a codon-restricted mRNA display and identified multiple de novo peptides from a peptide library that bind to poly(C) and poly(A) RNA with KDs ranging from micromolar to submicromolar concentrations. One of the newly identified peptides is capable of binding to the cytosine-rich sequences of the oncogenic Cdk6 3'UTR RNA and MYU lncRNA, with affinity comparable to that of the endogenous binding protein. Hence, we present a novel platform for discovering de novo single-stranded RNA-binding peptides that offer promising avenues for regulating RNA functions.

Biotechnology applications of proteins functionalized with DNA oligonucleotides

The functionalization of proteins with DNA through the formation of covalent bonds enables a wide range of biotechnology advancements. For example, single-molecule analytical methods rely on bioconjugated DNA as elastic biolinkers for protein immobilization. Labeling proteins with DNA enables facile protein identification, as well as spatial and temporal organization and control of protein within DNA-protein networks. Bioconjugation reactions can target native, engineered, and non-canonical amino acids (NCAAs) within proteins. In addition, further protein engineering via the incorporation of peptide tags and self-labeling proteins can also be used for conjugation reactions. The selection of techniques will depend on application requirements such as yield, selectivity, conjugation position, potential for steric hindrance, cost, commercial availability, and potential impact on protein function.

Assembly of Long-Adapter Single-Strand Oligonucleotide (LASSO) Probes for Massively Parallel Capture of Kilobase Size DNA Targets

Genome DNA sequencing has become an affordable means to resolve questions about the genetic background of life. However, the biological functions of many DNA-encoded sequences are still relatively unknown. A highly scalable and cost-effective cloning method to select natural DNA targets from genomic templates is therefore urgently needed to enable rapid understanding of the biological products of genomes. One such method involves LASSO probes, which are long single-stranded DNA oligonucleotides designed with a universal adapter that is used to link two sequences that are complementary to a genomic target of interest. Through a pooled assembly method, LASSOs can be made for multiplex DNA capture. Herein, we describe a robust, efficient method to assemble LASSO probe libraries using a Cre-recombinase-mediated reaction and a protocol for multiplex genome target capture. The starting components are a pre-LASSO probe library comprising short DNA oligo pools designed in silico and an Escherichia coli plasmid (pLASSO) that incorporates the pre-LASSO library. Through internal recombination of pLASSO with its inserts, a mature LASSO library in final configuration can be made with high purity. Assembly of a LASSO probe library takes 4 days, and target capture can be performed in a single day. With an exponentially growing list of new genomes available for investigation, this method can enable the rapid production of ORFeome libraries for high-throughput screening to identify biological functions as a complementary approach to understand genome functional biology. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Assembly of LASSO probes Support Protocol 1: Generation of pLASSO vectors Support Protocol 2: Preparation of pre-LASSOs Basic Protocol 2: Massively parallel capture of large DNAs using LASSO probes.

Applications of single-cell genomics and computational strategies to study common disease and population-level variation

The advent and rapid development of single-cell technologies have made it possible to study cellular heterogeneity at an unprecedented resolution and scale. Cellular heterogeneity underlies phenotypic differences among individuals, and studying cellular heterogeneity is an important step toward our understanding of the disease molecular mechanism. Single-cell technologies offer opportunities to characterize cellular heterogeneity from different angles, but how to link cellular heterogeneity with disease phenotypes requires careful computational analysis. In this article, we will review the current applications of single-cell methods in human disease studies and describe what we have learned so far from existing studies about human genetic variation. As single-cell technologies are becoming widely applicable in human disease studies, population-level studies have become a reality. We will describe how we should go about pursuing and designing these studies, particularly how to select study subjects, how to determine the number of cells to sequence per subject, and the needed sequencing depth per cell. We also discuss computational strategies for the analysis of single-cell data and describe how single-cell data can be integrated with bulk tissue data and data generated from genome-wide association studies. Finally, we point out open problems and future research directions.

A systematic review of the proteomic profile of in vivo acquired enamel pellicle on permanent teeth

OBJECTIVES

To provide a comprehensive review on the proteomic profile of in vivo acquired enamel pellicle (AEP) formed on permanent teeth.

DATA/SOURCES

PubMed, EMBASE (Ovid) and Web of Science databases were searched for eligible studies (up to December 2020). Studies reporting mass spectrometry-based proteomic analysis of in vivo AEP were included. Risk of bias assessment was performed. Qualitative and quantitative proteomic data were extracted, integrated, then followed by bioinformatic analysis.

STUDY SELECTION

Eleven studies were included, involving 122 systemically and dentally healthy adults from four different research groups. Pooled AEP samples from study participants were the normal practice for all included studies. A total of 257/93/108/870 non-redundant proteins were detectable from the in vivo ≤ 5 min/10-min/60-min/2-h AEP samples, respectively. Fifteen "core in vivo 2-h AEP proteins", generally associated with immune and/or inflammatory responses, were consistently identifiable from all four research groups. Eight included studies conducted relative quantitative proteomic analysis, while no statistical analysis could be undertaken due to the inherent limitation of the relative quantification in the proteomics analyses of these studies.

CONCLUSIONS

A systematic review on adult in vivo AEP proteomic profile was undertaken. The results provide a comprehensive appreciation of the AEP proteome in healthy individuals from in vivo sampling. Further studies are warranted to clarify the biological role of AEP on oral health, particularly at an individual level.

CLINICAL SIGNIFICANCE

A comprehensive appreciation of the proteomic profile of in vivo AEP in healthy individuals is essential to further understand its functions in oral health and disease. The information generated also provides insights for future studies.

Multiscale plant modeling: from genome to phenome and beyond

Plants are complex organisms that adapt to changes in their environment using an array of regulatory mechanisms that span across multiple levels of biological organization. Due to this complexity, it is difficult to predict emergent properties using conventional approaches that focus on single levels of biology such as the genome, transcriptome, or metabolome. Mathematical models of biological systems have emerged as useful tools for exploring pathways and identifying gaps in our current knowledge of biological processes. Identification of emergent properties, however, requires their vertical integration across biological scales through multiscale modeling. Multiscale models that capture and predict these emergent properties will allow us to predict how plants will respond to a changing climate and explore strategies for plant engineering. In this review, we (1) summarize the recent developments in plant multiscale modeling; (2) examine multiscale models of microbial systems that offer insight to potential future directions for the modeling of plant systems; (3) discuss computational tools and resources for developing multiscale models; and (4) examine future directions of the field.