Article
Computer Science, Artificial Intelligence
Mothe Rajesh, Sheshikala Martha
Summary: Single-cell RNA sequencing technology is utilized to analyze the transcriptomes of individual cells and identify rare cell populations. Traditional methods struggle to analyze transcriptomic profiles on a single-cell level, thus machine learning techniques have become crucial. In this study, we analyzed single-cell RNA sequencing data using linear dimensional reduction, identification of highly variable features, cell clustering, nonlinear dimensional reduction, and identification of gene markers. This analysis is important for identifying transcriptomic challenges and heterogeneity in cellular characteristics. Our research assists researchers in the field of bioinformatics and computational biology studying single-cell RNA sequencing data.
Article
Immunology
Emil Lagumdzic, Clara Pernold, Marta Viano, Simone Olgiati, Michael W. Schmitt, Kerstin H. Mair, Armin Saalmueller
Summary: Pigs have the potential to be a valuable research model for studying human diseases, pharmacology, and transplantation. This study aimed to better understand the porcine immune system by analyzing the transcriptomes of different subsets of porcine CD8(+) T cells. The results showed distinct gene expression patterns in different subsets, providing valuable information for further research on porcine immune cell subsets.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Multidisciplinary Sciences
Xu Shi, Xiao Wang, Andrew F. Neuwald, Leena Halakivi-Clarke, Robert Clarke, Jianhua Xuan
Summary: BayesDenovo addresses the challenge of de novo transcriptome assembly by accurately reconstructing splicing graphs using a read-guided and Bayesian strategy, achieving higher accuracy and reducing false positives, especially for alternatively spliced genes and highly/lowly expressed transcripts. Additionally, it is more robust on multiple replicates and can identify phenotype-specific transcripts associated with breast cancer recurrence.
SCIENTIFIC REPORTS
(2021)
Article
Multidisciplinary Sciences
August Guang, Mark Howison, Felipe Zapata, Charles Lawrence, Casey W. Dunn
Summary: treeinform is a method that utilizes phylogenetic information across species to improve transcriptome assemblies within species. It helps identify and correct the error of mistaking different transcripts of the same gene as transcripts from multiple closely related genes.
Article
Biochemical Research Methods
Qianqian Zhang, Xing Xu, Li Lin, Jian Yang, Xing Na, Xin Chen, Lingling Wu, Jia Song, Chaoyong Yang
Summary: Cilo-seq is a high-performance platform for single-cell RNA sequencing library construction. It utilizes digital microfluidics in a single device, enabling convenient single-cell isolation, efficient nucleic acid amplification, low-loss nucleic acid purification, and high-quality library preparation.
Article
Multidisciplinary Sciences
Chaoqiong Ding, Xiang Yan, Mengying Xu, Ran Zhou, Yuancun Zhao, Dan Zhang, Zongyao Huang, Zhenzhong Pan, Peng Xiao, Huifang Li, Lu Chen, Yuan Wang
Summary: This study reports the full-length transcriptome of mouse neural stem cells (NSCs) at different developmental stages, providing an important resource for studying NSC fate determination, neural development, and disease in the neuroscience community.
Article
Cell Biology
Di Wu
Summary: The germinal vesicle (GV) stage is a critical transition point in mammalian oocyte development that determines oocyte quality through active RNA degradation and transcriptome reprofiling. Oocyte RNA-seq has revealed differences between non-surrounded nucleolus (NSN) and surrounded nucleolus (SN) phases. Single oocyte RNA-seq (soRNA-seq) shows higher reproducibility and a better illustration of gene changes during oocyte development.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Immunology
Jingwen Deng, Carlotta Schieler, Jose A. M. Borghans, Chuanjian Lu, Aridaman Pandit
Summary: This study used a machine learning approach to explore the gene regulatory networks of psoriasis and identified key regulators. Interferon signaling was found to play a crucial role in psoriatic inflammation.
FRONTIERS IN IMMUNOLOGY
(2022)
Review
Genetics & Heredity
Wenbin Ye, Qiwei Lian, Congting Ye, Xiaohui Wu
Summary: Alternative polyadenylation (APA) plays important roles in modulating mRNA stability, translation, and subcellular localization, and contributes extensively to shaping eukaryotic transcriptome complexity and proteome diversity. In this article, we provide an exhaustive overview of computational approaches for predicting poly(A) sites (pAs) from DNA sequences, bulk RNA sequencing (RNA-seq) data, and single-cell RNA sequencing (scRNA-seq) data. We examine several representative tools and provide operable suggestions on assessing the reliability of pAs predicted by different tools. We also propose practical guidelines on choosing appropriate methods applicable to diverse scenarios and discuss the challenges and opportunities in improving pA prediction using new techniques.
GENOMICS PROTEOMICS & BIOINFORMATICS
(2023)
Article
Immunology
Toshio Kanno, Keisuke Miyako, Takahiro Nakajima, Satoru Yokoyama, Shigemi Sasamoto, Hikari K. Asou, Osamu Ohara, Toshinori Nakayama, Yusuke Endo
Summary: This study reveals that the decrease in monounsaturated fatty acid caused by the genetic deletion of Scd2 can activate IRF3 and induce the nuclear translocation of IRF9, leading to the production of type I interferon in CD4(+) Th1 cells. Furthermore, IRF9 selectively regulates autoimmunity-related genes in sgScd2 Th1 cells. These findings provide novel insights into the connection between fatty acid metabolism and immune response.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Immunology
Chenfeng He, Michael J. Malone, Ben S. Wendel, Ke-Yue Ma, Daniel Del Alcazar, David B. Weiner, Philip L. De Jager, Perla M. Del Rio-Estrada, Yuria Ablanedo-Terrazas, Gustavo Reyes-Teran, Laura F. Su, Ning Jiang
Summary: Follicular-helper T cells, a vital part of adaptive immunity, have complex and plastic functions, but study limitations have hindered a comprehensive understanding. CXCR3-expressing T-FH cells in chronic infection show abnormal accumulation in lymphoid tissues, suggesting potential functional differences that may enhance defense.
FRONTIERS IN IMMUNOLOGY
(2022)
Review
Biochemical Research Methods
Pablo Acera Mateos, You Zhou, Kathi Zarnack, Eduardo Eyras
Summary: The development of new high-throughput techniques has played a crucial role in discovering the properties of RNA modifications with the help of machine learning. Despite the challenges, this review provides a comprehensive survey of machine learning methods for detecting RNA modifications and strategies for training and testing these methods. The review also highlights current challenges and open questions in RNA modification analysis, and emphasizes the potential of machine learning in addressing these limitations.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Biotechnology & Applied Microbiology
Muchun Niu, Wenjian Cao, Yongcheng Wang, Qiangyuan Zhu, Jiayi Luo, Baiping Wang, Hui Zheng, David A. Weitz, Chenghang Zong
Summary: The profiling of individual synapses reveals molecular heterogeneity, which is crucial for signal transmission and shows considerable morphological and electrophysiological heterogeneity. However, there is currently a lack of high-throughput methods to analyze the molecular heterogeneity among individual synapses.
NATURE BIOTECHNOLOGY
(2023)
Article
Health Care Sciences & Services
Ana I. Oca, Alvaro Perez-Sala, Ana Pariente, Rodrigo Ochoa, Sara Velilla, Rafael Pelaez, Ignacio M. Larrayoz
Summary: AMD, an incurable disease associated with aging, is primarily treated with anti-VEGF agents through intravitreal injection. However, many patients do not respond satisfactorily to this treatment after three injections.
JOURNAL OF PERSONALIZED MEDICINE
(2021)
Article
Immunology
Venkatesh Kumaresan, Taylor MacMackin Ingle, Nathan Kilgore, Guoquan Zhang, Brian P. Hermann, Janakiram Seshu
Summary: By using single-cell RNA-Seq analysis, this study decoded the heterogeneity of splenocytes in C3H/HeN mice infected with Bb, revealing novel cellular features and signaling pathways associated with early immune responses against Bb. This finding contributes to limiting the transmission of Lyme disease to humans.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Genetics & Heredity
Lev Prasov, Brenda L. Bohnsack, Antonette S. El Husny, Lam C. Tsoi, Bin Guan, J. Michelle Kahlenberg, Edmundo Almeida, Haitao Wang, Edward W. Cowen, Adriana A. De Jesus, Priyam Jani, Allison C. Billi, Sayoko E. Moroi, Rachael Wasikowski, Izabela Almeida, Luciana N. Almeida, Fernando Kok, Sarah J. Garnai, Shahzad Mian, Marcus Y. Chen, Blake M. Warner, Carlos R. Ferreira, Raphaela Goldbach-Mansky, Sun Hur, Brian P. Brooks, Julia E. Richards, Robert B. Hufnagel, Johann E. Gudjonsson
Summary: Singleton-Merten syndrome (SGMRT) is a rare immunogenetic disorder characterized by features such as juvenile open-angle glaucoma, psoriasiform skin rash, and aortic calcifications. A study identified a novel DDX58 variant, expanding the genotypic spectrum of the disease. Furthermore, detailed ocular and dermatological phenotypes were described for the first time, shedding light on the molecular pathogenesis of SGMRT.
JOURNAL OF MEDICAL GENETICS
(2022)
Article
Allergy
Lam C. Tsoi, Matthew T. Patrick, Shao Shuai, Mrinal K. Sarkar, Sunyi Chi, Bethany Ruffino, Allison C. Billi, Xianying Xing, Ranjitha Uppala, Cheng Zang, Joseph Fullmer, Zhi He, Emanual Maverakis, Nehal N. Mehta, Bethany E. Perez White, Spiro Getsios, Yolanda Helfrich, John J. Voorhees, J. Michelle Kahlenberg, Stephan Weidinger, Johann E. Gudjonsson
Summary: This study evaluates the use of baseline molecular expression profiling to assess treatment outcome for patients with psoriasis. The results show a correlation between clinical response and molecular changes, particularly for genes responding to IL-17A/TNF in keratinocytes. Baseline gene expressions in nonlesional skin were found to be the best marker of treatment response, and cytokine gene signatures enriched in baseline nonlesional skin had strong correlations with treatment improvement.
JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY
(2022)
Article
Dermatology
Lam C. Tsoi, Xianying Xing, Enze Xing, Rachael Wasikowski, Shuai Shao, Chang Zeng, Olesya Plazyo, Joseph Kirma, Yanyung Jiang, Allison C. Billi, Mrinal K. Sarkar, Jessica L. Turnier, Ranjitha Uppala, Kathleen M. Smith, Yolanda Helfrich, John J. Voorhees, Emanual Maverakis, Robert L. Modlin, J. Michelle Kahlenberg, Victoria E. Scott, Johann E. Gudjonsson
Summary: This study demonstrates that tape stripping with optimized high-resolution transcriptomic profiling can effectively assess and characterize inflammatory responses in the skin. By comparing different samples and sampling methods, the study shows that tape stripping can capture the transcriptome of the upper layers of the skin, providing insights into the molecular components of the immune amplification pathway in psoriasis. Additionally, the study suggests that nonlesional psoriatic skin exhibits activated, proinflammatory changes, which are not captured by full-thickness skin biopsy transcriptome profiling.
JOURNAL OF INVESTIGATIVE DERMATOLOGY
(2022)
Article
Dermatology
Anna Klopot, Gleb Baida, Alexander Kel, Lam C. Tsoi, Bethany E. Perez White, Irina Budunova
Summary: Differences in gene expression between darkly pigmented and lightly pigmented skin were found, suggesting the existence of intrinsic proinflammatory circuits in darkly pigmented skin that may contribute to disease disparities. These findings provide a foundation for the development of targeted strategies for skin disease prevention.
JOURNAL OF INVESTIGATIVE DERMATOLOGY
(2022)
Article
Medicine, Research & Experimental
Garrett S. Dunlap, Allison C. Billi, Xianying Xing, Feiyang Ma, Mitra P. Maz, Lam C. Tsoi, Rachael Wasikowski, Jeffrey B. Hodgin, Johann E. Gudjonsson, J. Michelle Kahlenberg, Deepak A. Rao
Summary: This study provides a detailed single-cell RNA-Seq profile of T and NK cells in cutaneous lupus, revealing elevated expression of IFN-stimulated genes in T cells from lesional skin biopsies. While skin T cells from cutaneous lupus lesions did not show increased activation, cytotoxicity, or exhaustion compared to control skin, they did exhibit an elevated ISG signature compared to systemic sclerosis skin biopsies.
Article
Dermatology
Jiahe Wei, Jiahao Zhu, Huiqing Xu, Dan Zhou, James T. Elder, Lam C. Tsoi, Matthew T. Patrick, Yingjun Li
Summary: This study aimed to assess the causal associations of alcohol consumption and smoking with psoriasis risk. The findings revealed a causal effect of smoking on psoriasis risk, while no causal relationship was found between alcohol consumption and psoriasis. Restricting smoking could be helpful in reducing the burden of psoriasis.
BRITISH JOURNAL OF DERMATOLOGY
(2022)
Article
Genetics & Heredity
Matthew T. Patrick, Redina Bardhi, Wei Zhou, James T. Elder, Johann E. Gudjonsson, Lam C. Tsoi
Summary: This study demonstrates the utility of the UK Biobank as a population assay for rare diseases. By constructing a consensus mapping between ICD-10 codes and ORPHA codes and performing genetic association analysis, the researchers identified and characterized 420 rare diseases affecting individuals in the UK Biobank. Significant genetic associations for specific diseases were also identified. The study also highlights the transferability of the mapping method to other databases.
Article
Medicine, Research & Experimental
Alexander Merleev, Antonio Ji-Xu, Atrin Toussi, Lam C. Tsoi, Stephanie T. Le, Guillaume Luxardi, Xianying Xing, Rachael Wasikowski, William Liakos, Marie-Charlotte Brueggen, James T. Elder, Iannis E. Adamopoulos, Yoshihiro Izumiya, Annie R. Leal, Qinyuan Li, Nikolay Y. Kuzminykh, Amanda Kirane, Alina Marusina, Johann E. Gudjonsson, Emanual Maverakis
Summary: Using RNA-Seq-based variant discovery, a possible psoriasis-susceptibility locus was identified within the PCSK9 gene. Single-cell RNA-Seq analysis revealed that PCSK9 is primarily expressed in keratinocytes in human skin. The expression of PCSK9 varied across different keratinocyte subpopulations and showed an inverse relationship with IL36G expression. Furthermore, other immune genes were also found to be linked to PCSK9 expression.
Article
Medicine, Research & Experimental
Dinesh Khanna, Cristina Padilla, Lam C. Tsoi, Vivek Nagaraja, Puja P. Khanna, Tracy Tabib, J. Michelle Kahlenberg, Amber Young, Suiyuan Huang, Johann E. Gudjonsson, David A. Fox, Robert Lafyatis
Summary: This study found that the Janus kinase inhibitor tofacitinib was safe and well-tolerated in patients with early diffuse cutaneous systemic sclerosis (SSc). Gene expression analysis showed that tofacitinib inhibited inflammation in specific cell populations of SSc patients, indicating potential therapeutic effects. These findings are important for understanding the pathogenesis of SSc and developing new treatment strategies.
Article
Multidisciplinary Sciences
Matthew T. Patrick, Qinmengge Li, Rachael Wasikowski, Nehal Mehta, Johann E. Gudjonsson, James T. Elder, Xiang Zhou, Lam C. Tsoi
Summary: This study identifies shared genetic loci between psoriasis and coronary artery disease through trans-disease meta-analysis, and prioritizes genes associated with inflammatory signaling. It also suggests that chronic systemic inflammation can increase the risk of psoriasis and cause coronary artery disease.
NATURE COMMUNICATIONS
(2022)
Article
Dermatology
Alina I. Marusina, Antonio Ji-Xu, Stephanie T. Le, Atrin Toussi, Lam C. Tsoi, Qinyuan Li, Guillaume Luxardi, Jordan Nava, Lauren Downing, Annie R. Leal, Nikolay Y. Kuzminykh, Olga Kruglinskaya, Marie-Charlotte Bruggen, Iannis E. Adamopoulos, Alexander A. Merleev, Johann E. Gudjonsson, Emanual Maverakis
Summary: ERAP1, ERAP2, and LNPEP, which are aminopeptidases, play a role in autoimmune diseases. The expression of ERAP2 is increased while ERAP1 is decreased in psoriasis patients with autoimmune-linked variants of ERAP. Different layers of skin cells show different expression patterns of aminopeptidases, and in psoriasis, basal keratinocytes also express CCL2 and IL-15. In addition, ERAP2-high skin fibroblasts also express more CXCL14.
JOURNAL OF INVESTIGATIVE DERMATOLOGY
(2023)
Letter
Dermatology
Jake R. Saklatvala, Ken B. Hanscombe, Satveer K. Mahil, Lam C. Tsoi, James T. Elder, Jonathan N. Barker, Michael A. Simpson, Catherine H. Smith, Nick Dand
JOURNAL OF INVESTIGATIVE DERMATOLOGY
(2023)
Article
Dermatology
Henry W. Chen, Jane L. Zhu, Viktor Martyanov, Lam C. Tsoi, Michael E. Johnson, Grant Barber, Dillon Popovich, Jack C. O'Brien, Jennifer Coias, Nika Cyrus, Neeta Malviya, Stephanie Florez-Pollack, Elaine Kunzler, Gregory A. Hosler, Johann E. Gudjonsson, Dinesh Khanna, Michael Whitfield, Heidi T. Jacobe
Summary: Morphea is a skin-directed process characterized by T helper 1 immune-mediated dysregulation, which contrasts with fibrotic signatures and systemic transcriptional changes associated with systemic sclerosis. The similarity between morphea and the inflammatory subset of systemic sclerosis on transcriptional profiling indicates that therapies under development for this subset of systemic sclerosis are also promising for treatment of morphea.
JOURNAL OF INVESTIGATIVE DERMATOLOGY
(2023)
Letter
Dermatology
Kotaro Ogawa, Lam C. Tsoi, Hiroaki Tanaka, Masahiro Kanai, Philip E. Stuart, Rajan P. Nair, Yoshiya Tanaka, Hideki Mochizuki, James T. Elder, Yukinori Okada
JOURNAL OF INVESTIGATIVE DERMATOLOGY
(2023)
Article
Medicine, Research & Experimental
Lisa M. Godsel, Quinn R. Roth-Carter, Jennifer L. Koetsier, Lam C. Tsoi, Amber L. Huffine, Joshua A. Broussard, Gillian N. Fitz, Sarah M. Lloyd, Junghun Kweon, Hope E. Burks, Marihan Hegazy, Saki Amagai, Paul W. Harms, Xianying Xing, Joseph Kirma, Jodi L. Johnson, Gloria Urciuoli, Lynn T. Doglio, William R. Swindell, Rajeshwar Awatramani, Eli Sprecher, Xiaomin Bao, Eran Cohen-Barak, Caterina Missero, Johann E. Gudjonsson, Kathleen J. Green
Summary: Research reveals that genetic deficiency of Dsg1 causes a psoriatic-like inflammatory signature, and treatment with targeted therapy significantly improves skin lesions in patients.
JOURNAL OF CLINICAL INVESTIGATION
(2022)
