The sequence of the human genome

Potential mechanisms of non-coding RNA regulation in Alzheimer's disease

Alzheimer's disease, a progressively degenerative neurological disorder, is the most common cause of dementia in the elderly. While its precise etiology remains unclear, researchers have identified diverse pathological characteristics and molecular pathways associated with its progression. Advances in scientific research have increasingly highlighted the crucial role of non-coding RNAs in the progression of Alzheimer's disease. These non-coding RNAs regulate several biological processes critical to the advancement of the disease, offering promising potential as therapeutic targets and diagnostic biomarkers. Therefore, this review aims to investigate the underlying mechanisms of Alzheimer's disease onset, with a particular focus on microRNAs, long non-coding RNAs, and circular RNAs associated with the disease. The review elucidates the potential pathogenic processes of Alzheimer's disease and provides a detailed description of the synthesis mechanisms of the three aforementioned non-coding RNAs. It comprehensively summarizes the various non-coding RNAs that have been identified to play key regulatory roles in Alzheimer's disease, as well as how these non-coding RNAs influence the disease's progression by regulating gene expression and protein functions. For example, miR-9 targets the UBE4B gene, promoting autophagy-mediated degradation of Tau protein, thereby reducing Tau accumulation and delaying Alzheimer's disease progression. Conversely, the long non-coding RNA BACE1-AS stabilizes BACE1 mRNA, promoting the generation of amyloid-β and accelerating Alzheimer's disease development. Additionally, circular RNAs play significant roles in regulating neuroinflammatory responses. By integrating insights from these regulatory mechanisms, there is potential to discover new therapeutic targets and potential biomarkers for early detection and management of Alzheimer's disease. This review aims to enhance the understanding of the relationship between Alzheimer's disease and non-coding RNAs, potentially paving the way for early detection and novel treatment strategies.

Identification of deleterious non-synonymous single nucleotide polymorphisms in the mRNA decay activator ZFP36L2

More than 4,000 single nucleotide polymorphisms (SNP) variants have been identified in the human ZFP36L2 gene, however only a few have been studied in the context of protein function. The tandem zinc finger domain of ZFP36L2, an RNA binding protein, is the functional domain that binds to its target mRNAs. This protein/RNA interaction triggers mRNA degradation, controlling gene expression. We identified 32 non-synonymous SNPs (nsSNPs) in the tandem zinc finger domain of ZFP36L2 that could have possible deleterious impacts in humans. Using different bioinformatic strategies, we prioritized five among these 32 nsSNPs, namely rs375096815, rs1183688047, rs1214015428, rs1215671792 and rs920398592 to be validated. When we experimentally tested the functionality of these protein variants using gel shift assays, all five (Y154H, R160W, R184C, G204D, and C206F) resulted in a dramatic reduction in RNA binding compared to the WT protein. To understand the mechanistic effect of these variants on the protein/RNA interaction, we employed DUET, DynaMut and PyMOL to investigate structural changes in the protein. Additionally, we conducted Molecular Docking and Molecular Dynamics Simulations to fine tune the active behaviour of this biomolecular system at an atomic level. Our results propose atomic explanations for the impact of each of these five genetic variants identified.

Leading the Way: Multi-Drug Resistance Protein (MDR1) and Clinical Pharmacology-Commentary on Kim et al

Over the last three decades, transporters have become increasingly recognized for their important roles in clinical pharmacology. As gatekeepers of drug absorption, disposition and targeting, transporters in the intestine, liver, kidney and blood brain barrier have been the subject of many clinical pharmacology studies. A seminal work published in 2001 was among the first studies to shift the focus of pharmacogenomic research from drug metabolizing enzymes to drug transporters, demonstrating that pharmacogenomic factors in genes in addition to drug metabolizing enzymes, and in particular, in transporter genes, could play an important role in interindividual variation in pharmacokinetics of drugs.

Computer-Aided Drug Discovery for Undruggable Targets

Undruggable targets are those of therapeutical significance but challenging for conventional drug design approaches. Such targets often exhibit unique features, including highly dynamic structures, a lack of well-defined ligand-binding pockets, the presence of highly conserved active sites, and functional modulation by protein-protein interactions. Recent advances in computational simulations and artificial intelligence have revolutionized the drug design landscape, giving rise to innovative strategies for overcoming these obstacles. In this review, we highlight the latest progress in computational approaches for drug design against undruggable targets, present several successful case studies, and discuss remaining challenges and future directions. Special emphasis is placed on four primary target categories: intrinsically disordered proteins, protein allosteric regulation, protein-protein interactions, and protein degradation, along with discussion of emerging target types. We also examine how AI-driven methodologies have transformed the field, from applications in protein-ligand complex structure prediction and virtual screening to de novo ligand generation for undruggable targets. Integration of computational methods with experimental techniques is expected to bring further breakthroughs to overcome the hurdles of undruggable targets. As the field continues to evolve, these advancements hold great promise to expand the druggable space, offering new therapeutic opportunities for previously untreatable diseases.

SFRS8 Regulates Memory by Modulating RNA Splicing of Synaptic Genes

SFRS8, a member of the serine and arginine-rich (SR) protein family, functions as a splicing factor and is highly expressed in the brain. Despite its abundance, its specific role in the brain has remained unclear. Here, we show that SFRS8 is critical for maintaining normal synaptic protein levels and synaptic density. Mechanistically, SFRS8 binds to SF3B3, a key component of the U2 snRNP complex, to regulate alternative RNA splicing. Specifically, SFRS8 regulates the association of Psd95 pre-mRNA with the U2 snRNP complex and subsequent exon 18 skipping in Psd95, thereby controlling PSD95 protein levels. Knockdown of SFRS8 in the hippocampus reduces synaptic protein expression, decreases dendritic spine density, and impairs memory in mice. Consistent with these in vivo findings, SFRS8 depletion in cultured neurons also leads to lower synaptic protein levels and reduced synaptic density. Taken together, our results demonstrate that SFRS8 regulates memory function in mice by modulating the alternative splicing and expression of synaptic genes through its interaction with SF3B3, a core component of the U2 snRNP complex.

Investigating the Performance of Oxford Nanopore Long-Read Sequencing with Respect to Illumina Microarrays and Short-Read Sequencing

Oxford Nanopore Technologies (ONT) long-read sequencing (LRS) has emerged as a promising genomic analysis tool, yet comprehensive benchmarks with established platforms across diverse datasets remain limited. This study aimed to benchmark LRS performance against Illumina short-read sequencing (SRS) and microarrays for variant detection across different genomic contexts and to evaluate the impact of experimental factors. We sequenced 14 human genomes using the three platforms and evaluated single nucleotide variants (SNVs), insertions/deletions (indels), and structural variants (SVs) detection, stratifying by high-complexity, low-complexity, and dark genome regions while assessing effects of multiplexing, depth, and read length. LRS SNV accuracy was slightly lower than that of SRS in high-complexity regions (F-measure: 0.954 vs. 0.967) but showed comparable sensitivity in low-complexity regions. LRS showed robust performance for small (1-5 bp) indels in high-complexity regions (F-measure: 0.869), but SRS agreement decreased significantly in low-complexity regions and for larger indel sizes. Within dark regions, LRS identified more indels than SRS, but showed lower base-level accuracy. LRS identified 2.86 times more SVs than SRS, excelling at detecting large variants (>6 kb), with SV detection improving with sequencing depth. Sequencing depth strongly influenced variant calling performance, whereas multiplexing effects were minimal. Our findings provide valuable insights for optimising LRS applications in genomic research and diagnostics.

Toward clinical long-read genome sequencing for rare diseases

Genetic diagnostics is driven by technological advances, forming a tight interface between research, clinic and industry, which enables rapid implementation of new technologies. Short-read genome and exome sequencing, the current state of the art in clinical genetics, can detect a broad spectrum of genetic variants across the genome. However, despite these advancements, more than half of individuals with rare diseases remain undiagnosed after genomic investigations. Long-read whole-genome sequencing (LR-WGS) is a promising technology that identifies previously difficult-to-detect variants while also enabling phasing and methylation analysis and has the potential of generating complete personal assemblies. To pave the way for clinical use of LR-WGS, the clinical genomic community must establish standardized protocols and quality parameters while also developing innovative tools for data analysis and interpretation. In this Perspective, we explore the key challenges and benefits in integrating LR-WGS into routine clinical diagnostics.

Gene therapy then and now: A look back at changes in the field over the past 25 years

Since the inception of Molecular Therapy in 2000, the field of gene therapy has made remarkable progress, evolving from no approved clinical products to 23 clinical gene therapy products today. In this review, we aim to capture the transformative changes in the field by surveying the literature over this period, with a particular focus on advancements in gene delivery vector technology, disease and tissue targeting, and the revolutionary molecular tools that have become central to the field. We also discuss the current challenges facing gene therapy and the need for greater collaboration to ensure its accessibility worldwide.

Investigating the role of conformational heterogeneity in FUS-RRM fibrillation

The Fused in Sarcoma (FUS) protein, previously implicated in neurodegenerative diseases, contains N- and C-terminal LC-rich regions, a zinc finger motif flanked by two RG-rich regions, and a single RNA-recognition motif (RRM). FUS-RRM monomers undergo amyloid-like aggregation, however, the detailed molecular insights into the fibrillation process are yet to be deciphered. Here, we investigated the conformational heterogeneity of FUS-RRM using NMR relaxation-dispersion experiments. We observed that the monomer (M) exists in a dynamic exchange with an excited state (ES), which gets perturbed by altering the pH. Although the overall fold of the FUS-RRM remains unperturbed at the lower pH, aggregation kinetics increase. The data suggests a coupling of the conformational heterogeneity to aggregation kinetics wherein a perturbation to ES probably acts as a switch that controls the fibrillation process under physiological and stress conditions. These results add to the understanding of the fibrillation process, thereby paving the way for a better understanding of the role of FUS in neurodegenerative diseases.

Building better genome annotations across the tree of life

Recent technological advances in long-read DNA sequencing accompanied by reduction in costs have made the production of genome assemblies financially achievable and computationally feasible, such that genome assembly no longer represents the major hurdle to evolutionary analysis for most nonmodel organisms. Now, the more difficult challenge is to properly annotate a draft genome assembly once it has been constructed. The primary challenge to annotations is how to select from the myriad gene prediction tools that are currently available, determine what kinds of data are necessary to generate high-quality annotations, and evaluate the quality of the annotation. To determine which methods perform the best and to determine whether the inclusion of RNA-seq data is necessary to obtain a high-quality annotation, we generated annotations with 12 different methods for 21 different species spanning vertebrates, plants, and insects. We found that the annotation transfer method TOGA, BRAKER3, and the RNA-seq assembler StringTie were consistently top performers across a variety of metrics including BUSCO recovery, CDS length, and false-positive rate, with the exception that TOGA performed less well in some monocots with respect to BUSCO recovery. The choice of which of the top-performing methods will depend upon the feasibility of whole-genome alignment, availability of RNA-seq data, importance of capturing noncoding parts of the transcriptome, and, when whole-genome alignment is not feasible, the relative performance in BUSCO recovery between BRAKER3 and StringTie. When whole-genome alignment is not feasible, inclusion of RNA-seq data will lead to substantial improvements to genome annotations.

Complete sequencing of ape genomes

The most dynamic and repetitive regions of great ape genomes have traditionally been excluded from comparative studies1-3. Consequently, our understanding of the evolution of our species is incomplete. Here we present haplotype-resolved reference genomes and comparative analyses of six ape species: chimpanzee, bonobo, gorilla, Bornean orangutan, Sumatran orangutan and siamang. We achieve chromosome-level contiguity with substantial sequence accuracy (<1 error in 2.7 megabases) and completely sequence 215 gapless chromosomes telomere-to-telomere. We resolve challenging regions, such as the major histocompatibility complex and immunoglobulin loci, to provide in-depth evolutionary insights. Comparative analyses enabled investigations of the evolution and diversity of regions previously uncharacterized or incompletely studied without bias from mapping to the human reference genome. Such regions include newly minted gene families in lineage-specific segmental duplications, centromeric DNA, acrocentric chromosomes and subterminal heterochromatin. This resource serves as a comprehensive baseline for future evolutionary studies of humans and our closest living ape relatives.

Organ Donation for Research Biobanking Among Historically Marginalized Racial and Ethnic Groups: A Systematic Review

Importance

Research biobanks of human cells and tissues, particularly tissues accessible only after death, are crucial for advancing the understanding of human pathophysiological function. Research biobanks are bereft of tissues from individuals of diverse races and ethnicities, thus limiting the generalizability of biobank findings.

Objective

To evaluate the barriers and facilitators to participation in postmortem brain donation for research among individuals from historically marginalized races and ethnicities.

Evidence Review

The published literature in PubMed, Embase, Web of Science, and PsycINFO databases was searched from 1973 to January 1, 2024. Studies that were written in English that involved adult participants (aged ≥18 years) and explored attitudes, perceptions, and beliefs on solid organ donation were included. Studies in which organ donation was for transplant and not for research, studies examining pediatric organ donation, narratives or perspectives, and studies that did not examine attitudes or beliefs toward organ donation were excluded. Two authors independently coded and performed a thematic analysis of eligible studies.

Findings

Eighteen studies met the inclusion criteria, which involved 12 124 participants across multiple self-reported races and ethnicities (eg, Black or African American, Chinese, Hispanic or Latiné, and White). Most studies (16 [89%]) evaluated perceptions, attitudes, and beliefs among Black or African American and Hispanic or Latiné individuals toward postmortem brain donation. Five themes that informed the decision to donate were identified: information and misconceptions about the organ donation process (16 studies [89%]), mistrust of the research and medical communities (9 studies [50%]), family involvement (9 studies [50%]), religious and cultural beliefs (9 studies [50%]), and altruism (7 studies [39%]). Mistrust and religious and cultural beliefs were largely barriers to considering postmortem organ donation for research. Misconceptions were common, particularly regarding the donation process and purpose of biospecimens for research. Family involvement was both a barrier and a facilitator. Altruism, particularly understanding that organ donation would benefit the participants' family, future generations, and community, was a facilitator.

Conclusions and Relevance

This systematic review suggests that sharing culturally sensitive information about the organ donation process, engagement of participants and family members in shared decision-making, and addressing barriers and facilitators to donor recruitment practices may increase participation in research biobanks of individuals from underrepresented racial and ethnic groups.

An industrial available platform for high-yield, plasmid-free recombinant protein production in E. coli based on advanced cSAT scheme

Protein production is a cornerstone of biotechnology, and the cleavable self- aggregating tag (cSAT) scheme has been developed for column-free purification of recombinant proteins. We present an advanced cSAT (acSAT) scheme for high-yield recombinant protein production in E. coli. The acSAT scheme integrates a linker between the intein and target protein, reducing premature cleavage and enhancing protein yield. We screened ten linkers, optimizing the cleavage efficiency and yield of model proteins such as collagen type III (COL-III), fibronectin (FN), and fusion proteins (FP). Further optimization using dual-linkers resulted in improved yields of truncated COL-III (tCOL-III), with dual-linker L13 increasing the yield of tCOL-III by 119 %. Additionally, we identified a high-performing neutral genomic integration site near the oriC of E. coli with integration efficiency nearly 100 %, enabling plasmid-free, antibiotic-free expression systems for large-scale production. In 5-L fed-batch fermentation, acSAT scheme yielded up to 1.51 g/L tCOL-III, which was 27.2 times higher than that of shake flask cultures. This platform offers a cost-effective, scalable solution for industrial recombinant protein production.

Cryoelectron microscopy as a tool for illuminating activation mechanisms of human class A orphan G protein-coupled receptors

G protein-coupled receptors (GPCRs) are critically important medicinal targets, and the cryogenic electron microscopy (cryo-EM) revolution is providing novel high-resolution GPCR structures at a rapid pace. Orphan G protein-coupled receptors (oGPCRs) are a group of approximately 100 nonolfactory GPCRs for which endogenous ligands are unknown or not validated. The absence of modulating ligands adds difficulties to understanding the physiologic significance of oGPCRs and in the determination of high-resolution structures of isolated receptors that could facilitate drug discovery. Despite the challenges, cryo-EM structures of oGPCR-G protein complexes are emerging. This is being facilitated by numerous developments to stabilize GPCR-G protein complexes such as the use of dominant-negative G proteins, mini-G proteins, complex-stabilizing nanobodies or antibody fragments, and protein tethering methods. Moreover, many oGPCRs are constitutively active, which can facilitate complex formation in the absence of a known activating ligand. Consequently, in addition to providing templates for drug discovery, active oGPCR structures shed light on constitutive GPCR activation mechanisms. These comprise self-activation, whereby mobile extracellular portions of the receptor act as tethered agonists by occupying a canonical orthosteric-binding site in the transmembrane core, constitutive activity due to alterations to conserved molecular switches that stabilize inactive states of GPCRs, as well as receptors activated by cryptic ligands that are copurified with the receptor. Cryo-EM structures of oGPCRs are now being determined at a rapid pace and are expected to be invaluable tools for oGPCR drug discovery. SIGNIFICANCE STATEMENT: Orphan G protein-coupled receptors (GPCRs) provide large untapped potential for development of new medicines. Many of these receptors display constitutive activity, enabling structure determination and insights into observed GPCR constitutive activity including (1) self-activation by mobile receptor extracellular portions that function as tethered agonists, (2) modification of conserved motifs canonically involved in receptor quiescence and/or activation, and (3) activation by cryptic lipid ligands. Collectively, these studies advance fundamental understanding of GPCR function and provide opportunities for novel drug discovery.

Harnessing Noncanonical Proteins for Next-Generation Drug Discovery and Diagnosis

Noncanonical proteins, encoded by previously overlooked genomic regions (part of the "dark genome"), are emerging as crucial players in human health and disease, expanding our understanding of the "dark proteome." This review explores their landscape, including proteins derived from long non-coding RNAs, circular RNAs, and alternative open reading frames. Recent advances in ribosome profiling, mass spectrometry, and proteogenomics have unveiled their involvement in critical cellular processes. We examine their roles in cancer, neurological disorders, cardiovascular diseases, and infectious diseases, highlighting their potential as novel biomarkers and therapeutic targets. The review addresses challenges in identifying and characterizing these proteins, particularly recently evolved ones, and discusses implications for drug discovery, including cancer immunotherapy and neoantigen sources. By synthesizing recent findings, we underscore the significance of noncanonical proteins in expanding our understanding of the human genome and proteome, and their promise in developing innovative diagnostic tools and targeted therapies. This overview aims to stimulate further research into this unexplored biological space, potentially revolutionizing approaches to disease treatment and personalized medicine.

My NGS and Other Animals

High-throughput sequencing is one of a number of omics technologies that generates huge amounts of data in the form of nucleotide sequences [...].

Establishing genome sequencing and assembly for non-model and emerging model organisms: a brief guide

Reference genome assemblies are the basis for comprehensive genomic analyses and comparisons. Due to declining sequencing costs and growing computational power, genome projects are now feasible in smaller labs. De novo genome sequencing for non-model or emerging model organisms requires knowledge about genome size and techniques for extracting high molecular weight DNA. Next to quality, the amount of DNA obtained from single individuals is crucial, especially, when dealing with small organisms. While long-read sequencing technologies are the methods of choice for creating high quality genome assemblies, pure short-read assemblies might bear most of the coding parts of a genome but are usually much more fragmented and do not well resolve repeat elements or structural variants. Several genome initiatives produce more and more non-model organism genomes and provide rules for standards in genome sequencing and assembly. However, sometimes the organism of choice is not part of such an initiative or does not meet its standards. Therefore, if the scientific question can be answered with a genome of low contiguity in intergenic parts, missing the high standards of chromosome scale assembly should not prevent publication. This review describes how to set up an animal genome sequencing project in the lab, how to estimate costs and resources, and how to deal with suboptimal conditions. Thus, we aim to suggest optimal strategies for genome sequencing that fulfil the needs according to specific research questions, e.g. "How are species related to each other based on whole genomes?" (phylogenomics), "How do genomes of populations within a species differ?" (population genomics), "Are differences between populations relevant for conservation?" (conservation genomics), "Which selection pressure is acting on certain genes?" (identification of genes under selection), "Did repeats expand or contract recently?" (repeat dynamics).

[Individualization and standardization in head and neck pathology]

Individualization and standardization are seemingly contradictory requirements in medicine. In the treatment of head and neck cancer, both terms have a direct influence on diagnostic procedures, which are usually carried out in pathology institutes. The current article examines the conflicting requirements arising from various technical analyses, regulatory requirements, structural changes due to digitalization, and the advent of personalized medicine. On the one hand, the goal is to promote interdisciplinary exchange by understanding the challenges and, on the other, to provide the otorhinolaryngologist with a practical understanding of the common and current pathological diagnostic tests. Using pathology as an example, it can be shown that standardization of procedures ultimately serves to improve individualized treatment. At the same time, however, the following challenges are also apparent: despite comprehensive regulations and a laboratory environment with digital support, standardization is very time consuming and costly. If similar standardization approaches are to be implemented in an operative environment such as, e.g., ENT surgery, the effort involved can be expected to be equivalent or higher due to the human factor.

The Druggable Transcriptome Project: From Chemical Probes to Precision Medicines

RNA presents abundant opportunities as a drug target, offering significant potential for small molecule medicine development. The transcriptome, comprising both coding and noncoding RNAs, is a rich area for therapeutic innovation, yet challenges persist in targeting RNA with small molecules. RNA structure can be predicted with or without experimental data, but discrepancies with the actual biological structure can impede progress. Prioritizing RNA targets supported by genetic or evolutionary evidence enhances success. Further, small molecules must demonstrate binding to RNA in cells, not solely in vitro, to validate both the target and compound. Effective small molecule binders modulate functional sites that influence RNA biology, as binding to nonfunctional sites requires recruiting effector mechanisms, for example degradation, to achieve therapeutic outcomes. Addressing these challenges is critical to unlocking RNA's vast potential for small molecule medicines, and a strategic framework is proposed to navigate this promising field, with a focus on targeting human RNAs.

Host ZAP activity correlates with the levels of CpG suppression in primate lentiviruses

Zinc-finger antiviral protein (ZAP) is thought to drive the suppression of CpG dinucleotides in many viruses to mimic the composition of their host genomes. However, in vivo evidence is sparse. Here, we investigated the reasons for unusually high CpG levels in SIVmus and SIVmon from mustached and mona monkeys, descendants of one of the precursors of HIV-1. We show that SIVmus is not resistant to ZAP inhibition. Instead, these Cercopithecus monkey hosts differ from other primate species by a splice site mutation and express the poorly active extralarge XL rather than the highly active L isoform of ZAP. Similarly, higher CpG levels in endogenous prosimian lentiviruses were associated with low activity of the corresponding host lemur ZAPs. In addition, lemur genes also show lower CpG suppression than other primates. Thus, the antiviral activity of ZAP not only affects suppression of CpG dinucleotides in viral transcripts but possibly also host genomes.

Effect of Alternative Splicing Euchromatic Histone Lysine Methyltransferase 2 (EHMT2/G9A) on Spermatogenesis in Mongolian Horses

The epigenetic regulation of gene expression through the covalent modification of histones is crucial for developing germline cells. To study the regulatory role of alternative splicing (AS) of euchromatic histone lysine methyltransferase 2 (EHMT2/G9A) in spermatogenesis in Mongolian horses, this study first examines the localization of the EHMT2 gene in testicular support cells and then predicts the higher-order structures of sequences with and without AS. Two types of lentiviral vectors for overexpression were subsequently constructed for the EHMT2 gene, one with AS and one without, to infect support cells. The proliferation and activity of infected cells were measured using CCK8, and the differential expression of spermatogenesis-related genes in the two types of support cells was analyzed via qRT-PCR. We analyzed the expression of EHMT2 by immunofluorescence staining. EHMT2 was expressed in the nuclei of Sertoli cells. The expression of spermatogenesis-related genes was measured in the two types of cells. The results reveal that the expression levels of the FSH, Stra8, CCNB2, CDC27, NRG1, PPP2R5C, CCNB2, and YWHAZ genes in the AS group were greater than those in the control group. These results indicate that AS events in EHMT2 affect gene expression and thus affect spermatogenesis.

Treating the individual: moving towards personalised eating disorder care

Eating disorders (EDs) are complex and heterogeneous conditions, which are often not resolved with conventional, manualised treatments. Arguments for the development of holistic, person-centred treatments accounting for individual variability have been mounting amongst researchers, clinicians and people with lived experience alike. This review explores the transformative potential of personalised medicine in ED care, emphasising the integration of precision diagnostics and tailored interventions based on individual genetic, biological, psychological and environmental profiles. Building on advancements in genomics, neurobiology, and computational technologies, it advocates for a shift from categorical diagnostic frameworks to symptom-based and dimensional approaches. The paper summarises emerging evidence supporting precision psychiatry, including the development of biomarkers, patient-reported outcomes, predictive modelling, and staging models, and discusses their application in ED research and clinical care. It highlights the utility of machine learning and idiographic statistical methods in optimising therapeutic outcomes and identifies key challenges, such as ethical considerations, scalability and implementation.

The Gut Mycobiome for Precision Medicine

The human gastrointestinal tract harbors a vast array of microorganisms, which play essential roles in maintaining metabolic balance and immune function. While bacteria dominate the gut microbiome, fungi represent a much smaller, often overlooked fraction. Despite their relatively low abundance, fungi may significantly influence both health and disease. Advances in next-generation sequencing, metagenomics, metatranscriptomics, metaproteomics, metabolomics, and computational biology have provided novel opportunities to study the gut mycobiome, shedding light on its composition, functional genes, and metabolite interactions. Emerging evidence links fungal dysbiosis to various diseases, including inflammatory bowel disease, colorectal cancer, metabolic disorders, and neurological conditions. The gut mycobiome also presents a promising avenue for precision medicine, particularly in biomarker discovery, disease diagnostics, and targeted therapeutics. Nonetheless, significant challenges remain in effectively integrating gut mycobiome knowledge into clinical practice. This review examines gut fungal microbiota, highlighting analytical methods, associations with human diseases, and its potential role in precision medicine. It also discusses pathways for clinical translation, particularly in diagnosis and treatment, while addressing key barriers to implementation.

Systems biology of dry eye: Unraveling molecular mechanisms through multi-omics integration

Dry eye disease (DED) is a multifactorial condition with complex and incompletely understood molecular mechanisms. Advances in multi-omics technologies, including genomics, transcriptomics, proteomics, metabolomics, and microbiomics, have provided new insights into the pathophysiology of DED. Genomic analyses have identified key genetic variants linked to immune regulation and lacrimal gland function. Transcriptomic studies reveal upregulated inflammatory pathways in ocular surface tissues, implicating these as core drivers of chronic inflammation. Proteomic research highlights significant alterations in tear protein composition, especially proteins involved in inflammation and tissue repair. Metabolomics studies focus on disrupted lipid metabolism and oxidative stress, which are crucial in maintaining tear film stability. Furthermore, microbiome research has demonstrated reduced microbial diversity and increased pathogenic bacteria, exacerbating inflammatory responses. The integration of multi-omics data allows for the identification of novel biomarkers and therapeutic targets, enabling precision diagnostics and personalized treatments. Therefore, this review highlights the critical importance of multi-omics approaches in deepening our understanding of DED's complex molecular mechanisms and their potential to transform clinical management and therapeutic innovations in this challenging field.

Advances in cancer genomics and precision oncology

BACKGROUND

Next-generation sequencing has revolutionized genome science over the last two decades. Indeed, the wealth of sequence information on our genome has deepened our understanding on cancer. Cancer is a genetic disease caused by genetic or epigenetic alternations that affect the expression of genes that control cell functions, particularly cell growth and division. Utilization of next-generation sequencing in cancer gene panels has enabled the identification of actionable gene alterations in cancer patients to guide personalized precision medicine.

OBJECTIVE

The aim is to provide information that can identify actionable gene alterations, enabling personalized precision medicine for cancer patients.

RESULTS & DISCUSSION

Equipped with next-generation sequencing techniques, international collaboration programs on cancer genomics have identified numerous mutations, gene fusions, microsatellite variations, copy number variations, and epigenetics changes that promote the transformation of normal cells into tumors. Cancer classification has traditionally been based on cell type or tissue-of-origin and the morphological characteristics of the cancer. However, interactive genomic analyses have currently reclassified cancers based on systemic molecular-based taxonomy. Although all cancer-causing genes and mechanisms have yet to be completely understood or identified, personalized or precision medicine is now currently possible for some forms of cancer. Unlike the "one-size-fits-all" approach of traditional medicine, precision medicine allows for customized or personalized treatment based on genomic information.

CONCLUSION

Despite the availability of numerous cancer gene panels, technological innovation in genomics and expansion of knowledge on the cancer genome will allow precision oncology to manage even more types of cancers.

Structural insights into the dual Ca2+-sensor-mediated activation of the PPEF phosphatase family

Serine/threonine-protein phosphatases with EF-hands (PPEFs) are a family of highly conserved proteins implicated in cancer and neuronal degeneration. The initially characterized member, Drosophila melanogaster retinal degeneration C (RDGC) contains a calmodulin (CaM)-interacting extended-IQ motif and a Ca2+-binding EF-like/EF-hand tandem. However, the molecular regulation of PPEF is poorly understood. In this study, we use cryogenic-electron microscopy to delineate the structures of the RDGC/CaM holoenzyme. In the absence of Ca2+, CaM and the EF-like/EF-hand tandem allow the extended-IQ motif to block substrate access to the catalytic sites, constituting an auto-inhibitory mechanism. Upon Ca2+ binding, CaM and the EF-like/EF-hand tandem drive drastic conformational changes in the extended-IQ motif to unlock the catalytic sites. This dual Ca2+-sensor-mediated activation is evolutionarily conserved in mammals. This study provides mechanistic insight into the molecular activation of PPEFs, paving the way for the development of therapeutic strategies for PPEF-related human diseases.

Differences in DPYD Population Frequencies Observed in Galicians Compared to Europeans and Spanish from PhotoDPYD Study

Background/Objectives: Fluoropyrimidine derivatives, 5-fluorouracil (5-FU) and its prodrugs (capecitabine and tegafur), are widely used in patients suffering from colorectal cancer. The enzyme responsible for their metabolization, dihydropyrimidine dehydrogenase (DPD), is encoded by the DPYD gene, which is highly polymorphic and may contain polymorphisms which could severely compromise its function. This article aims to describe the prevalence of the four main DPYD polymorphisms in the Galician population (Spain) and to compare these frequencies with data obtained from European cohorts in genetic databases and a Spanish study. Methods: Galician data frequencies for the four main DPYD polymorphisms recommended by the European Medicine Agency (EMA) and the Spanish Agency for Medicines and Health Products (AEMPS) (rs3918290 (c.1905+1G>A), rs55886062 (c.1679T>G), rs56038477 (c.1236G>A) and rs67376798 (c.2846A>T)) were collected, as well as data from the genomic databases 1000 Genomes and gnomAD. Additionally, the results from a Spanish DPYD study were included. Results: Significant differences in DPYD variant allele frequencies were observed in the Galician population compared to the frequencies reported in the European population, as well as in the Spanish PhotoDPYD study. Specifically, the rs56038477-T variant (most prevalent) along with the rs3918290-T variant, exhibited significantly lower frequencies than anticipated in the Galician cohort, with a high degree of statistical significance. Conclusions: Observed allele frequencies for the four DPYD variants suggest that Europeans and Spanish frequencies may not be fully applicable to the Galician population. These results emphasize the emerging need for incorporating the genetic information of populations that might be underrepresented into populational databases available worldwide.

Decoding Immunobiology Through Genetic Errors of Immunity

Throughout biology, the pursuit of genotype-phenotype relationships has provided foundational knowledge upon which new concepts and hypotheses are built. Genetic perturbation, whether occurring naturally or in experimental settings, is the mainstay of mechanistic dissection in biological systems. The unbiased discovery of causal genetic lesions via forward genetics in patients who have a rare disease elucidates a particularly impactful set of genotype-phenotype relationships. Here, we review the field of genetic errors of immunity, often termed inborn errors of immunity (IEIs), in a framework aimed at highlighting the powerful real-world immunology insights provided collectively and individually by these (approximately) 500 disorders. By conceptualizing essential immune functions in a model of the adaptive arsenal of rapid defenses, we organize IEIs based on immune circuits in which sensors, relays, and executioners cooperate to carry out pathogen clearance functions in an effective yet regulated manner. We review and discuss findings from IEIs that not only reinforce known immunology concepts but also offer surprising phenotypes, prompting an opportunity to refine our understanding of immune system function.

Nucleic Acid Therapy for the Skin

Advances in sequencing technologies have facilitated the identification of the genes and mechanisms for many inherited skin diseases. Although targeted nucleic acid therapeutics for diseases in other organs have begun to be deployed in patients, the goal of precise therapeutics for skin diseases has not yet been realized. First, we review the current and emerging nucleic acid-based gene-editing and delivery modalities. Next, current and emerging viral and nanoparticle vehicles for the delivery of gene therapies are reviewed. Finally, specific skin diseases that could benefit optimally from nucleic acid therapies are highlighted. By adopting the latest technologies and addressing specific barriers related to skin biology, nucleic acid therapeutics have the potential to revolutionize treatments for patients with skin disease.

A compendium of human gene functions derived from evolutionary modelling

A comprehensive, computable representation of the functional repertoire of all macromolecules encoded within the human genome is a foundational resource for biology and biomedical research. The Gene Ontology Consortium has been working towards this goal by generating a structured body of information about gene functions, which now includes experimental findings reported in more than 175,000 publications for human genes and genes in experimentally tractable model organisms1,2. Here, we describe the results of a large, international effort to integrate all of these findings to create a representation of human gene functions that is as complete and accurate as possible. Specifically, we apply an expert-curated, explicit evolutionary modelling approach to all human protein-coding genes. This approach integrates available experimental information across families of related genes into models that reconstruct the gain and loss of functional characteristics over evolutionary time. The models and the resulting set of 68,667 integrated gene functions cover approximately 82% of human protein-coding genes. The functional repertoire reveals a marked preponderance of molecular regulatory functions, and the models provide insights into the evolutionary origins of human gene functions. We show that our set of descriptions of functions can improve the widely used genomic technique of Gene Ontology enrichment analysis. The experimental evidence for each functional characteristic is recorded, thereby enabling the scientific community to help review and improve the resource, which we have made publicly available.

Measures of Homozygosity and Relationship to Genetic Diversity in the Bearded Collie Breed

Background: Genetic diversity in closed populations, such as pedigree dogs, is of concern for maintaining the health and vitality of the population in the face of evolving challenges. Measures of genetic diversity rely upon estimates of homozygosity without consideration of whether the homozygosity is desirable or undesirable or if heterozygosity has a functional impact. Pedigree coefficients of inbreeding have been the classical approach yet they are inadequate unless based upon the entire population. Methods: Homozygosity measures based upon pedigree analyses (n = 11,898), SNP array data (n = 244), and whole genome sequencing (n = 23) were compared in the Bearded Collie, as well as a comparison of SNP array data to a pedigree cohort (n = 5042) and a mixed-breed cohort (n = 1171). Results: Molecular measures based upon DNA are more informative on an individual's homozygosity levels than pedigree analyses, although SNP coefficients of inbreeding overestimate the level of inbreeding based on the nature of SNP array methodology. Whole genome sequence (WGS) analyses revealed that the heterozygosity observed is generally in variants having neutral or low impact, which would indicate that the variability may not contribute substantially to functional diversity in the population. The majority of high-impact variants were observed in the shortest runs of homozygosity (ROH) reflecting ancestral breeding and domestication practices. As expected, mixed-breed dogs displayed higher measures of genomic diversity than either Bearded Collies or other pedigree dogs as a whole using the current paradigm algorithm models to calculate homozygosity. Conclusions: Using typical DNA-based measures reflect only a single individual and not the population thereby failing to account for regions of homozygosity that reflect ancestral breeding, domestication history, breed-defining regions, or regions positively selected for health traits. Incorporating measures of genetic diversity into dog breeding schemes is meritorious. However, until measures of diversity can distinguish between breed-defining homozygosity and homozygosity associated with positive health alleles, the measures to use as selection tools need refinement before their widespread implementation.

Genome-wide association studies, Polygenic Risk Scores and Mendelian randomisation: an overview of common genetic epidemiology methods for ophthalmic clinicians

Genetic information will be increasingly integrated into clinical eye care within the current generation of ophthalmologists. For monogenic diseases such as retinoblastoma, genetic studies have been relatively straightforward as these conditions result from pathogenic variants in a single gene resulting in large physiological effects. However, most eye diseases result from the cumulative effects of multiple genetic variants and environmental factors. In such diseases, because each variant usually has an individually small effect, genetic studies for complex diseases are comparatively more challenging. This article aims to provide an overview of three genetic epidemiology methods for polygenic (or complex) diseases: genome-wide association studies (GWAS), Polygenic Risk Scores (PRS) and Mendelian randomisation (MR). A GWAS systematically conducts association analyses of a trait of interest against millions of genetic variants, usually in the form of single nucleotide polymorphisms, across the genome. GWAS findings can then be used for PRS construction and MR analyses. To construct a PRS, the cumulative effect of many genetic variants associated with a trait from a prior GWAS is calculated and taken as a quantitative representation of an individual's genetic risk of a complex disease. MR studies analyse an outcome measure against the genetic variants of an exposure, and are particularly useful in investigating causal relations between two traits where randomised controlled trials are not possible or ethical. In addition to explaining the principles of these three genetic epidemiology concepts, this article provides a minimally technical description of their basic methodology that is accessible to the non-expert reader.

In-Depth Comparison of Reagent-Based Digestion Methods and Two Commercially Available Kits for Bottom-Up Proteomics

Proteomic analysis plays an essential role in biology with several methodologies available for sample preparation and analysis. This study evaluates and compares various cell lysis and protein digestion protocols for bottom-up proteomics using HeLa S3 cells. We assessed two physical disruption methods to homogenize cells-sonication and BeatBox-alongside four digestion protocols. Two of them are lab-reagent strategies: urea-based and sodium deoxycholate (SDC)-based in-solution digestion, and two are commercially available kits: the EasyPep kit from Thermo Fisher Scientific and S-Trap from Protifi. Each method's efficacy was evaluated based on protein recovery, peptide yield, and number of unique proteins identified through LC-MS analysis. Our results indicate that while both sonication and the BeatBox (PreOmics Inc.) methods provided comparable protein recovery and coverage, the choice of digestion method had a much bigger impact on the amount of protein IDs found. SDC digestion yielded the highest protein and peptide counts, while S-Trap exhibited the most consistent peptide recovery. Conversely, EasyPep showed higher variability in peptide recovery, with a ±10% difference in the average peptide number. Each homogenization strategy and digestion method also yielded its own list of unique proteins. These results provide several lists of proteins for biologists to select from based on experimental needs and highlight the importance of choosing appropriate protocols for comprehensive proteomic analyses.

K-mer-based Approaches to Bridging Pangenomics and Population Genetics

Many commonly studied species now have more than one chromosome-scale genome assembly, revealing a large amount of genetic diversity previously missed by approaches that map short reads to a single reference. However, many species still lack multiple reference genomes and correctly aligning references to build pangenomes can be challenging for many species, limiting our ability to study this missing genomic variation in population genetics. Here, we argue that k-mers are a very useful but underutilized tool for bridging the reference-focused paradigms of population genetics with the reference-free paradigms of pangenomics. We review current literature on the uses of k-mers for performing three core components of most population genetics analyses: identifying, measuring, and explaining patterns of genetic variation. We also demonstrate how different k-mer-based measures of genetic variation behave in population genetic simulations according to the choice of k, depth of sequencing coverage, and degree of data compression. Overall, we find that k-mer-based measures of genetic diversity scale consistently with pairwise nucleotide diversity (π) up to values of about π=0.025 (R2=0.97) for neutrally evolving populations. For populations with even more variation, using shorter k-mers will maintain the scalability up to at least π=0.1. Furthermore, in our simulated populations, k-mer dissimilarity values can be reliably approximated from counting bloom filters, highlighting a potential avenue to decreasing the memory burden of k-mer-based genomic dissimilarity analyses. For future studies, there is a great opportunity to further develop methods to identifying selected loci using k-mers.

HEK-omics: The promise of omics to optimize HEK293 for recombinant adeno-associated virus (rAAV) gene therapy manufacturing

Gene therapy is poised to transition from niche to mainstream medicine, with recombinant adeno-associated virus (rAAV) as the vector of choice. However, robust, scalable, industrialized production is required to meet demand and provide affordable patient access, which has not yet materialized. Closing the chasm between demand and supply requires innovation in biomanufacturing to achieve the essential step change in rAAV product yield and quality. Omics provides a rich source of mechanistic knowledge that can be applied to HEK293, the most commonly used cell line for rAAV production. In this review, the findings from a growing number of diverse studies that apply genomics, epigenomics, transcriptomics, proteomics, and metabolomics to HEK293 bioproduction are explored. Learnings from CHO-omics, application of omics approaches to improve CHO bioproduction, provide a framework to explore the potential of "HEK-omics" as a multi-omics-informed approach providing actionable mechanistic insights for improved transient and stable production of rAAV and other recombinant products in HEK293.

Role of the human cytochrome b561 family in iron metabolism and tumors (Review)

The human cytochrome b561 (hCytb561) family consists of electron transfer transmembrane proteins characterized by six conserved α-helical transmembrane domains and two β-type heme cofactors. These proteins contribute to the regulation of iron metabolism and numerous different physiological and pathological processes by recycling ascorbic acid and maintaining iron reductase activity. Key members of this family include cytochrome b561 (CYB561), duodenal CYB561 (Dcytb), lysosomal CYB561 (LCytb), stromal cell-derived receptor 2 (SDR2) and 101F6, which are widely expressed in human tissues and participate in the pathogenesis of several diseases and tumors. They are associated with the promotion or inhibition of tumor growth and progression in various malignancies and are potential therapeutic targets for malignant tumors. The present review summarizes the existing literature regarding the structure of the Cytb561 family, the basic functional characteristics of hCytb561 family members, and the roles of the CYB561, Dcytb, LCytb, SDR2 and 101F6 in various diseases and tumors.

PDX models for functional precision oncology and discovery science

Precision oncology relies on detailed molecular analysis of how diverse tumours respond to various therapies, with the aim to optimize treatment outcomes for individual patients. Patient-derived xenograft (PDX) models have been key to preclinical validation of precision oncology approaches, enabling the analysis of each tumour's unique genomic landscape and testing therapies that are predicted to be effective based on specific mutations, gene expression patterns or signalling abnormalities. To extend these standard precision oncology approaches, the field has strived to complement the otherwise static and often descriptive measurements with functional assays, termed functional precision oncology (FPO). By utilizing diverse PDX and PDX-derived models, FPO has gained traction as an effective preclinical and clinical tool to more precisely recapitulate patient biology using in vivo and ex vivo functional assays. Here, we explore advances and limitations of PDX and PDX-derived models for precision oncology and FPO. We also examine the future of PDX models for precision oncology in the age of artificial intelligence. Integrating these two disciplines could be the key to fast, accurate and cost-effective treatment prediction, revolutionizing oncology and providing patients with cancer with the most effective, personalized treatments.

RNA binding proteins (RBPs) on genetic stability and diseases

RNA-binding proteins (RBPs) are integral components of cellular machinery, playing crucial roles in the regulation of gene expression and maintaining genetic stability. Their interactions with RNA molecules govern critical processes such as mRNA splicing, stability, localization, and translation, which are essential for proper cellular function. These proteins interact with RNA molecules and other proteins to form ribonucleoprotein complexes (RNPs), hence controlling the fate of target RNAs. The interaction occurs via RNA recognition motif, the zinc finger domain, the KH domain and the double stranded RNA binding motif (all known as RNA-binding domains (RBDs). These domains are found within the coding sequences (intron and exon domains), 5' untranslated regions (5'UTR) and 3' untranslated regions (3'UTR). Dysregulation of RBPs can lead to genomic instability, contributing to various pathologies, including cancer neurodegenerative diseases, and metabolic disorders. This study comprehensively explores the multifaceted roles of RBPs in genetic stability, highlighting their involvement in maintaining genomic integrity through modulation of RNA processing and their implications in cellular signalling pathways. Furthermore, it discusses how aberrant RBP function can precipitate genetic instability and disease progression, emphasizing the therapeutic potential of targeting RBPs in restoring cellular homeostasis. Through an analysis of current literature, this study aims to delineate the critical role of RBPs in ensuring genetic stability and their promise as targets for innovative therapeutic strategies.

Growth in a two-dimensional model of coarctation of the aorta: A CFD-informed agent based model

In the individualized treatment of a patient with Coarctation of the Aorta (CoA), a non-severe case which initially exhibits no symptoms, and thus requires no treatment, could potentially become severe over time. This progression can be attributed to insufficient growth at the coarctation site relative to the overall growth of the child. Therefore, an agent-based model (ABM) to predict the aortic growth of a CoA patient is introduced. The multi-scale approach combines Computational Fluid Dynamics (CFD) and ABM to study systems that are influenced by both mechanical stimuli and biochemical responses characteristic of growth. Our focus is on ABM development; thus, CFD insights were applied solely to enhance the ABM framework. Comparative medicine was leveraged to develop a species-specific ABM by considering the rat and porcine species commonly used in cardiovascular research together with data from healthy human toddlers. The ABM luminal radius prediction accuracy was observed to be 79% for rat, above 95% for porcine and 91. 6% for the healthy toddler; while that observed for the growth rate was 38.7%, 90% and 64.3% respectively. Given its performance, the ABM was adapted to a 2.5-year-old patient-specific CoA. Subsequently, the model predicted that by age 3, the condition would worsen, marked by persistent CoA enhanced by the predicted least growth compared to growth predicted in the rest of the aorta, hypertension, and increased turbulent flow; thus, increased vessel injury risk. The findings advise for incorporating vascular remodelling into the ABM to enhance its predictive capability for intervention planning.

Noncoding RNA-encoded peptides in cancer: biological functions, posttranslational modifications and therapeutic potential

In the present era, noncoding RNAs (ncRNAs) have become a subject of considerable scientific interest, with peptides encoded by ncRNAs representing a particularly promising avenue of investigation. The identification of ncRNA-encoded peptides in human cancers is increasing. These peptides regulate cancer progression through multiple molecular mechanisms. Here, we delineate the patterns of diverse ncRNA-encoded peptides and provide a synopsis of the methodologies employed for the identification of ncRNAs that possess the capacity to encode these peptides. Furthermore, we discuss the impacts of ncRNA-encoded peptides on the biological behavior of cancer cells and the underlying molecular mechanisms. In conclusion, we describe the prospects of ncRNA-encoded peptides in cancer and the challenges that need to be overcome.

Polymerase Chain Reaction: A Toolbox for Molecular Discovery

Polymerase chain reaction (PCR), a revolutionary molecular tool, has transformed genetic studies by facilitating rapid DNA amplification. The PCR process relies on several key components: a DNA template or cDNA, two primers, Taq polymerase, nucleotides, and a buffer. These elements collectively facilitate the amplification process, which comprises three stages: denaturation, annealing, and extension. These stages are repeated in cycles to exponentially amplify the target DNA sequence. Furthermore, the power of PCR lies in its ability to generate exponential copies of target DNA in a remarkably short period. Moreover, various PCR techniques are available, encompassing traditional approaches like quantitative PCR, reverse transcription PCR, and nested PCR, as well as innovative methods such as extreme PCR, inverse PCR, and touchdown PCR. These techniques are extensively utilized in molecular, biological, and medical research laboratories for both research and diagnostic applications. This review explores a comprehensive overview of PCR, covering its history, underlying principles, and diverse applications in diagnostics, research, and drug development.

Multi-ancestry GWAS reveals loci linked to human variation in LINE-1- and Alu-insertion numbers

LINE-1 (L1) and Alu are two families of transposable elements (TEs) occupying ~17% and ~11% of the human genome, respectively. Though only a small fraction of L1 copies is able to produce the machinery to mobilize autonomously, Alu and degenerate L1s can hijack their functional machinery and mobilize in trans. The expression and subsequent mobilization of L1 and Alu can exert pathological effects on their hosts. These features have made them promising focus subjects in studies of aging where they can become active. However, mechanisms regulating TE activity are incompletely characterized, especially in diverse human populations. To address these gaps, we leveraged genomic data from the 1000 Genomes Project to carry out a trans-ethnic GWAS of L1/Alu insertion singletons. These are rare, recently acquired insertions observed in only one person and which we used as proxies for variation in L1/Alu insertion numbers. Our approach identified SNVs in genomic regions containing genes with potential and known TE regulatory properties, and it enriched for SNVs in regions containing known regulators of L1 expression. Moreover, we identified reference TE copies and structural variants that associated with L1/Alu singletons, suggesting their potential contribution to TE insertion number variation. Finally, a transcriptional analysis of lymphoblastoid cells highlighted potential cell cycle alterations in a subset of samples harboring L1/Alu singletons. Collectively, our results suggest that known TE regulatory mechanisms may be active in diverse human populations, expand the list of loci implicated in TE insertion number variability, and reinforce links between TEs and disease.

Past, present, and future strategies for detecting and quantifying circular RNA variants

Circular RNAs (circRNAs) are a family of covalently closed RNA transcripts ubiquitous across the eukaryotic kingdom. CircRNAs are generated by a class of alternative splicing called backsplicing, with the resultant circularization of a part of parental RNA producing the characteristic backsplice junction (BSJ). Because of the noncontiguous sequence of the BSJ with respect to the DNA genome, circRNAs remained hidden in plain sight through over a decade of RNA next-generation sequencing, yet over 3 million unique circRNA transcripts have been illuminated in the past decade alone. CircRNAs are expressed in a cell type-specific manner, are highly stable, with many examples of circRNAs being evolutionarily conserved and/or functional in specific contexts. However, circRNAs can be very lowly expressed and predictions of the circRNA context from BSJ-spanning reads alone can confound extrapolation of the exact sequence composition of the circRNA transcript. For these reasons, specific and ultrasensitive detection, combined with enrichment, bespoke bioinformatics pipelines and, more recently, long-read, highly processive sequencing is becoming critical for complete characterization of all circRNA variants. Concomitantly, the need for targeted detection and quantification of specific circRNAs has sparked numerous laboratory-based and commercial approaches to visualize circRNAs in cells and quantify them in biological samples, including biospecimens. This review focuses on advancements in the detection and quantification of circRNAs, with a particular focus on recent next-generation sequencing approaches to bolster detection of circRNA variants and accurately normalize between sequencing libraries.

Data Readout Techniques for DNA-Based Information Storage

DNA is a natural chemical substrate that carries genetic information, which also serves as a powerful toolkit for storing digital data. Compared to traditional storage media, DNA molecules offer higher storage density, longer lifespan, and lower maintenance energy consumption. In DNA storage process, data readout is a critical step that bridges the gap between DNA molecular/structures with stored digital information. With the continued development of strategies in DNA data storage technology, the readout techniques have evolved. However, there is a lack of systematic introduction and discussion on the readout techniques for reported DNA data storage systems, especially the correlation between the design of the data storage system and the corresponding selection of readout techniques. This review first introduces two main categories of DNA data storage units (i.e., sequence and structure) and their corresponding readout techniques (i.e., sequencing and nonsequencing methods), and then reviewed representative examples of notable advancements in DNA data storage technology, focusing on data storage unit design, and readout technique selection. It also introduces emerging approaches to assist data readout techniques, such as implementation of microfluidic and fluorescent probes. Finally, the paper discusses the limitations, challenges, and potential of DNA data readout approaches.

Accurate assembly of full-length consensus for viral quasispecies

BACKGROUND

Viruses can inhabit their hosts in the form of an ensemble of various mutant strains. Reconstructing a robust consensus representation for these diverse mutant strains is essential for recognizing the genetic variations among strains and delving into aspects like virulence, pathogenesis, and selecting therapies. Virus genomes are typically small, often composed of only a few thousand to several hundred thousand nucleotides. While constructing a high-quality consensus of virus strains might seem feasible, most current assemblers only generated fragmented contigs. It's important to emphasize the significance of assembling a single full-length consensus contig, as it's vital for identifying genetic diversity and estimating strain abundance accurately.

RESULTS

In this paper, we developed FC-Virus, a de novo genome assembly strategy specifically targeting highly diverse viral populations. FC-Virus first identifies the k-mers that are common across most viral strains, and then uses these k-mers as a backbone to build a full-length consensus sequence covering the entire genome. We benchmark FC-Virus against state-of-the-art genome assemblers.

CONCLUSION

Experimental results confirm that FC-Virus can construct a single, accurate full-length consensus, whereas other assemblers only manage to produce fragmented contigs. FC-Virus is freely available at https://github.com/qdu-bioinfo/FC-Virus.git .

Insights into eye genetics and recent advances in ocular gene therapy

The rapid advancements in the field of genetics have significantly propelled the development of gene therapies, paving the way for innovative treatments of various hereditary disorders. This review focuses on the genetics of ophthalmologic conditions, highlighting the currently approved ophthalmic gene therapy and exploring emerging therapeutic strategies under development. Inherited retinal dystrophies represent a heterogeneous group of genetic disorders that manifest across a broad spectrum from infancy to late middle age. Key clinical features include nyctalopia (night blindness), constriction of the visual field, impairments in color perception, reduced central visual acuity, and rapid eye movements. Recent technological advancements, such as multimodal imaging, psychophysical assessments, and electrophysiological testing, have greatly enhanced our ability to understand disease progression and establish genotype-phenotype correlations. Additionally, the integration of molecular diagnostics into clinical practice is revolutionizing patient stratification and the design of targeted interventions, underscoring the transformative potential of personalized medicine in ophthalmology. The review also covers the challenges and opportunities in developing gene therapies for other ophthalmic conditions, such as age-related macular degeneration and optic neuropathies. We discuss the viral and non-viral vector systems used in ocular gene therapy, highlighting their advantages and limitations. Additionally, we explore the potential of emerging technologies like CRISPR/Cas9 in treating genetic eye diseases. We briefly address the regulatory landscape, concerns, challenges, and future directions of gene therapy in ophthalmology. We emphasize the need for long-term safety and efficacy data as these innovative treatments move from bench to bedside.

MorPhiC Consortium: towards functional characterization of all human genes

Recent advances in functional genomics and human cellular models have substantially enhanced our understanding of the structure and regulation of the human genome. However, our grasp of the molecular functions of human genes remains incomplete and biased towards specific gene classes. The Molecular Phenotypes of Null Alleles in Cells (MorPhiC) Consortium aims to address this gap by creating a comprehensive catalogue of the molecular and cellular phenotypes associated with null alleles of all human genes using in vitro multicellular systems. In this Perspective, we present the strategic vision of the MorPhiC Consortium and discuss various strategies for generating null alleles, as well as the challenges involved. We describe the cellular models and scalable phenotypic readouts that will be used in the consortium's initial phase, focusing on 1,000 protein-coding genes. The resulting molecular and cellular data will be compiled into a catalogue of null-allele phenotypes. The methodologies developed in this phase will establish best practices for extending these approaches to all human protein-coding genes. The resources generated-including engineered cell lines, plasmids, phenotypic data, genomic information and computational tools-will be made available to the broader research community to facilitate deeper insights into human gene functions.

Impact of commercial RNA extraction methods on the recovery of human RNA sequence data from archival fixed tissues

Archival fixed tissues hold key insights into the evolutionary history of RNA viruses and the associated host immune response, yet access to the RNA sequence data is limited by a lack of robust methods for RNA extraction and sequence retrieval from these tissue types. Here we compared three commercial RNA extraction techniques (bead, column, and phase-based) on five fixed human brain tissues done in triplicate, that have been stored for up to 43 years. We found that for this sample set, bead-based extractions captured longer molecules and yielded a greater proportion of unique reads when aligned to the human genome, than did column and phase-based extraction methods. Via the incorporation of multiple extraction replicates, we quantified the variability in sequencing metrics resulting from tissue sample and extraction technique heterogeneity. Additionally, we compared pre- and post-sequencing metrics and found that the former poorly predicted post-sequencing on-target success. Our findings help inform future research on the recovery of RNA from archival fixed tissues.

Perspectives and opportunities in forensic human, animal, and plant integrative genomics in the Pangenome era

The Human Pangenome Reference Consortium, the Chinese Pangenome Consortium, and other plant and animal pangenome projects have announced the completion of pilot work aimed at constructing high-quality, haplotype-resolved reference graph genomes representative of global ethno-linguistically different populations or different plant and animal species. These graph-based, gapless pangenome references, which are enriched in terms of genomic diversity, completeness, and contiguity, have the potential for enhancing long-read sequencing (LRS)-based genomic research, as well as improving mappability and variant genotyping on traditional short-read sequencing platforms. We comprehensively discuss the advancements in pangenome-based genomic integrative genomic discoveries across forensic-related species (humans, animals, and plants) and summarize their applications in variant identification and forensic genomics, epigenetics, transcriptomics, and microbiome research. Recent developments in multiplexed array sequencing have introduced a highly efficient and programmable technique to overcome the limitations of short forensic marker lengths in LRS platforms. This technique enables the concatenation of short RNA transcripts and DNA fragments into LRS-optimal molecules for sequencing, assembly, and genotyping. The integration of new pangenome reference coordinates and corresponding computational algorithms will benefit forensic integrative genomics by facilitating new marker identification, accurate genotyping, high-resolution panel development, and the updating of statistical algorithms. This review highlights the necessity of integrating LRS-based platforms, pangenome-based study designs, and graph-based pangenome references in short-read mapping and LRS-based innovations to achieve precision forensic science.