{"title":"Multiplexed multimodal single-cell technologies: From observation to perturbation analysis","authors":"Su-Hyeon Lee , Junha Park , Byungjin Hwang","doi":"10.1016/j.mocell.2024.100147","DOIUrl":"10.1016/j.mocell.2024.100147","url":null,"abstract":"<div><div>Single-cell technologies have undergone a significant transformation, expanding from their initial focus on transcriptomics to encompass a diverse range of modalities. Recent advancements have markedly improved scalability and reduced costs, facilitating the processing of larger cell populations and broadening the scope of single-cell research. The incorporation of clustered regularly interspaced short palindromic repeats (CRISPR)-based perturbations has revolutionized the field by enabling precise functional genomics and detailed studies of gene regulation at the single-cell level. Despite these advancements, challenges persist, particularly in achieving genome-wide perturbations and managing the complexity of high-throughput data. This review discusses the technological milestones that have driven these changes, the current limitations of single-cell CRISPR technologies, and the future directions needed to address these challenges and advance our understanding of cellular biology.</div></div>","PeriodicalId":18795,"journal":{"name":"Molecules and Cells","volume":"47 12","pages":"Article 100147"},"PeriodicalIF":3.7,"publicationDate":"2024-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142624106","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
June Yeon Kim, Kyeongho Lee, Moon Geon Lee, Sung-Jin Kim
{"title":"Periodontitis and atherosclerotic cardiovascular disease","authors":"June Yeon Kim, Kyeongho Lee, Moon Geon Lee, Sung-Jin Kim","doi":"10.1016/j.mocell.2024.100146","DOIUrl":"10.1016/j.mocell.2024.100146","url":null,"abstract":"<div><div>Atherosclerotic cardiovascular disease (ASCVD) is a major global health concern linked to significant morbidity and mortality. Recent research has explored the relationship between ASCVD and periodontitis, a prevalent inflammatory oral condition. Epidemiological studies have suggested a strong association between periodontitis and ASCVD, even proposing that periodontal disease could be a modifiable risk factor for cardiovascular conditions. This review critically analyzes the current evidence for a potential causal role for periodontitis in ASCVD. While randomized controlled trials have demonstrated reductions in surrogate markers of cardiovascular risk following periodontal interventions, these studies remain inconclusive regarding their direct effects on cardiovascular events. Preclinical studies in animal models have suggested a potential causal relationship between periodontitis and ASCVD, proposing several biological mechanisms to explain this connection. These studies, however, are limited in their ability to definitively prove causality. The positive associations observed in epidemiological studies between periodontitis and ASCVD may also be influenced by various biases, such as confounding and collider stratification. Moreover, our systematic review of Mendelian randomization studies on the causal relationship between periodontitis and ASCVD found no evidence of a genetic causality, further challenging the causal hypothesis. This review underscores the need for further high-quality research clarifying the relationship between periodontitis and ASCVD to better guide clinical practice and public health policy.</div></div>","PeriodicalId":18795,"journal":{"name":"Molecules and Cells","volume":"47 12","pages":"Article 100146"},"PeriodicalIF":3.7,"publicationDate":"2024-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142624109","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Seung Hye Lee, Ji Sun Jang, Shenzheng Mo, Hong-Hee Kim
{"title":"TMEM175 plays a crucial role in osteoblast differentiation by regulating lysosomal function and autophagy","authors":"Seung Hye Lee, Ji Sun Jang, Shenzheng Mo, Hong-Hee Kim","doi":"10.1016/j.mocell.2024.100127","DOIUrl":"10.1016/j.mocell.2024.100127","url":null,"abstract":"<div><div>Bone provides structural support, enables movement, protects internal organs, regulates calcium and phosphorus levels, and contains bone marrow essential for hematopoiesis. Osteoblasts are specialized cells responsible for bone formation through the secretion of extracellular matrix components. Transmembrane protein 175 (TMEM175), which functions as an endosomal/lysosomal K<sup>+</sup> channel and a lysosomal H<sup>+</sup> channel, regulates lysosomal function and autophagy. Despite the recognized importance of lysosomes and autophagy in osteoblast differentiation, the specific role of TMEM175 in osteoblast differentiation has not been revealed. In this study, we investigated whether TMEM175 is associated with human bone mineral density and fracture and examined the role of TMEM175 in osteoblast differentiation. In analyses of single nucleotide polymorphisms of pore ion channel genes using the mouse2human database, a significant correlation between TMEM175 single nucleotide polymorphisms and human bone mineral density and fracture was identified. TMEM175 expression levels were found to increase during osteoblast differentiation from bone chip-derived mesenchymal stem cells (BMSCs). Knockdown of TMEM175 in BMSCs suppressed osteoblast differentiation, as evidenced by decreased matrix mineralization and lower expression levels of osteoblast marker genes. Further analysis indicated that TMEM175 deficiency leads to lysosomal dysfunction and partially impairs autophagic clearance during osteoblast differentiation. Moreover, the TMEM175 inhibitor 4-aminopyridine decreased osteoblast differentiation of BMSCs. Taken together, this study reveals that TMEM175 plays an important role in osteoblast differentiation by regulating lysosomal function and autophagic clearance.</div></div>","PeriodicalId":18795,"journal":{"name":"Molecules and Cells","volume":"47 11","pages":"Article 100127"},"PeriodicalIF":3.7,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142470234","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Cover and caption","authors":"","doi":"10.1016/S1016-8478(24)00178-X","DOIUrl":"10.1016/S1016-8478(24)00178-X","url":null,"abstract":"","PeriodicalId":18795,"journal":{"name":"Molecules and Cells","volume":"47 11","pages":"Article 100153"},"PeriodicalIF":3.7,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142704437","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Yeeun Choi, Eun-Seon Yoo, Youjin Oh, Jong-Woo Sohn
{"title":"Cellular and metabolic function of GIRK1 potassium channels expressed by arcuate POMC and NPY/AgRP neurons","authors":"Yeeun Choi, Eun-Seon Yoo, Youjin Oh, Jong-Woo Sohn","doi":"10.1016/j.mocell.2024.100122","DOIUrl":"10.1016/j.mocell.2024.100122","url":null,"abstract":"<div><div>It is well known that the G protein-gated inwardly rectifying K<sup>+</sup> (GIRK) channels are critical to maintain excitability of central neurons. GIRK channels consist of 4 subunits and GIRK1/GIRK2 heterotetramers are considered to be the neuronal prototype. We previously reported the metabolic significance of GIRK2 subunits expressed by the neuropeptide Y (NPY)/agouti-related peptide (AgRP) neurons of the arcuate nucleus of the hypothalamus (ARH). However, the role of GIRK1 subunits expressed by the neurons of ARH remains to be determined. In this study, we delineated the contribution of GIRK1 channel subunits to the excitability of the pro-opiomelanocortin (POMC) and NPY/AgRP neurons of the ARH. We further assessed the metabolic function of GIRK1 subunits expressed by these neurons. Our results provide insight into how GIRK channels regulate arcuate POMC and NPY/AgRP neurons and shape metabolic phenotypes.</div></div>","PeriodicalId":18795,"journal":{"name":"Molecules and Cells","volume":"47 11","pages":"Article 100122"},"PeriodicalIF":3.7,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142391898","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"A brief guide to analyzing expression quantitative trait loci","authors":"Byung Su Ko , Sung Bae Lee , Tae-Kyung Kim","doi":"10.1016/j.mocell.2024.100139","DOIUrl":"10.1016/j.mocell.2024.100139","url":null,"abstract":"<div><div>Molecular quantitative trait locus (molQTL) mapping has emerged as an important approach for elucidating the functional consequences of genetic variants and unraveling the causal mechanisms underlying diseases or complex traits. However, the variety of analysis tools and sophisticated methodologies available for molQTL studies can be overwhelming for researchers with limited computational expertise. Here, we provide a brief guideline with a curated list of methods and software tools for analyzing expression quantitative trait loci, the most widely studied type of molQTL.</div></div>","PeriodicalId":18795,"journal":{"name":"Molecules and Cells","volume":"47 11","pages":"Article 100139"},"PeriodicalIF":3.7,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142504290","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"The emerging role of gut hormones","authors":"Hyeryeong Cho , Jaechul Lim","doi":"10.1016/j.mocell.2024.100126","DOIUrl":"10.1016/j.mocell.2024.100126","url":null,"abstract":"<div><div>The gut is traditionally recognized as the central organ for the digestion and absorption of nutrients, however, it also functions as a significant endocrine organ, secreting a variety of hormones such as glucagon-like peptide 1, serotonin, somatostatin, and glucocorticoids. These gut hormones, produced by specialized intestinal epithelial cells, are crucial not only for digestive processes but also for the regulation of a wide range of physiological functions, including appetite, metabolism, and immune responses. While gut hormones can exert systemic effects, they also play a pivotal role in maintaining local homeostasis within the gut. This review discusses the role of the gut as an endocrine organ, emphasizing the stimuli, the newly discovered functions, and the clinical significance of gut-secreted hormones. Deciphering the emerging role of gut hormones will lead to a better understanding of gut homeostasis, innovative treatments for disorders in the gut, as well as systemic diseases.</div></div>","PeriodicalId":18795,"journal":{"name":"Molecules and Cells","volume":"47 11","pages":"Article 100126"},"PeriodicalIF":3.7,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142470233","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Sung Ho Boo , Min-Kyung Shin , Hongseok Ha , Jae-Sung Woo , Yoon Ki Kim
{"title":"Transcriptome-wide analysis for glucocorticoid receptor-mediated mRNA decay reveals various classes of target transcripts","authors":"Sung Ho Boo , Min-Kyung Shin , Hongseok Ha , Jae-Sung Woo , Yoon Ki Kim","doi":"10.1016/j.mocell.2024.100130","DOIUrl":"10.1016/j.mocell.2024.100130","url":null,"abstract":"<div><div>The glucocorticoid receptor (GR) can bind to DNA or RNA, eliciting transcriptional activation/repression or rapid messenger RNA (mRNA) degradation, respectively. Although GR-mediated transcriptional regulation has been well-characterized, the molecular details of rapid mRNA degradation induced by glucocorticoids are not yet fully understood. Here, we demonstrate that glucocorticoid-induced GR-mediated mRNA decay (GMD) takes place in the nucleus and the cytoplasm, acting on pre-mRNAs and mRNAs. We also performed cross-linking and immunoprecipitation coupled with high-throughput sequencing analysis for GMD factors (GR, YBX1, and HRSP12) and mRNA sequencing analysis to identify endogenous GMD substrates. Our comprehensive coupled with high-throughput sequencing and mRNA sequencing analyses reveal that a range of cellular transcripts containing a common binding site for GR, YBX1, and HRSP12 are preferential targets for GMD, suggesting possible new functions of GMD in various biological events.</div></div>","PeriodicalId":18795,"journal":{"name":"Molecules and Cells","volume":"47 11","pages":"Article 100130"},"PeriodicalIF":3.7,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142470235","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}