Garber Lab Publications

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ABOUT THIS COLLECTION

This collection showcases journal articles and other publications produced by researchers in the Garber Lab. The Garber Lab at UMass Chan Medical School was established in 2012, in the Program in Bioinformatics and Integrative Biology, which evolved into the Department of Genomics and Computational Biology in 2023.

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Recent Publications

  • Publication
    Single cell RNA-sequencing reveals molecular signatures that distinguish allergic from irritant contact dermatitis
    (2024-09-26) Frisoli, Michael L; Ko, Wei-Che C; Martinez, Nuria; Afshari, Khashayar; Wang, Yuqing; Garber, Manuel; Harris, John E; Dermatology; Genomics and Computational Biology; Morningside Graduate School of Biomedical Sciences; Garber Lab; Michael L Frisoli; Yuqing Wang
    Allergic contact dermatitis (ACD) is a pruritic skin disease caused by environmental chemicals that induce cell-mediated skin inflammation within susceptible individuals. Irritant contact dermatitis (ICD) is caused by direct damage to the skin barrier by environmental insults. Diagnosis can be challenging as both types of contact dermatitis can appear similar by visual exam, and histopathological analysis does not reliably distinguish ACD from ICD. To discover specific biomarkers of ACD and ICD, we characterized the transcriptomic and proteomic changes that occur within the skin during each type of contact dermatitis. We induced ACD and ICD in healthy human volunteers and sampled skin using a non-scarring suction blister biopsy method that collects interstitial fluid and cellular infiltrate. Single cell RNA-sequencing analysis revealed that cell-specific transcriptome differences rather than cell type proportions best distinguished ACD from ICD. Allergy-specific genes were associated with upregulation of IFNG, and cell signaling network analysis implicated several other genes such as IL4, despite their low expression levels. We validated transcriptomic differences with proteomic assays on blister fluid and trained a logistic regression model on skin interstitial fluid proteins that could distinguish ACD from ICD and healthy control skin with 93% sensitivity and 93% specificity.
  • Publication
    Systemic and skin-limited delayed-type drug hypersensitivity reactions associate with distinct resident and recruited T cell subsets
    (2024-07-23) Shah, Pranali N; Romar, George A; Manukyan, Artür; Ko, Wei-Che; Hsieh, Pei-Chen; Velasquez, Gustavo A; Schunkert, Elisa M; Fu, Xiaopeng; Guleria, Indira; Bronson, Roderick T; Wei, Kevin; Waldman, Abigail H; Vleugels, Frank R; Liang, Marilyn G; Giobbie-Hurder, Anita; Mostaghimi, Arash; Schmidt, Birgitta Ar; Barrera, Victor; Foreman, Ruth K; Garber, Manuel; Divito, Sherrie J; Dermatology; Genomics and Computational Biology; Garber Lab
    Delayed-type drug hypersensitivity reactions are major causes of morbidity and mortality. The origin, phenotype and function of pathogenic T cells across the spectrum of severity requires investigation. We leveraged recent technical advancements to study skin-resident memory T cells (TRM) versus recruited T cell subsets in the pathogenesis of severe systemic forms of disease, SJS/TEN and DRESS, and skin-limited disease, morbilliform drug eruption (MDE). Microscopy, bulk transcriptional profiling and scRNAseq + CITEseq + TCRseq supported in SJS/TEN clonal expansion and recruitment of cytotoxic CD8+ T cells from circulation into skin, along with expanded and non-expanded cytotoxic CD8+ skin TRM. Comparatively, MDE displayed a cytotoxic T cell profile in skin without appreciable expansion and recruitment of cytotoxic CD8+ T cells from circulation, implicating TRM as potential protagonists in skin-limited disease. Mechanistic interrogation in patients unable to recruit T cells from circulation into skin and in a parallel mouse model supported that skin TRM were sufficient to mediate MDE. Concomitantly, SJS/TEN displayed a reduced regulatory T cell (Treg) signature compared to MDE. DRESS demonstrated recruitment of cytotoxic CD8+ T cells into skin like SJS/TEN, yet a pro-Treg signature like MDE. These findings have important implications for fundamental skin immunology and clinical care.
  • Publication
    An Early Islet Transcriptional Signature Is Associated With Local Inflammation in Autoimmune Diabetes
    (2022-11-08) Derr, Alan G; Arowosegbe, Adediwura; Satish, Basanthi; Redick, Sambra D; Qaisar, Natasha; Guo, Zhiru; Vanderleeden, Emma; Trombly, Melanie I; Baer, Christina E; Harlan, David M; Greiner, Dale L; Garber, Manuel; Wang, Jennifer P; Diabetes Center of Excellence; Medicine; Microbiology and Physiological Systems; Morningside Graduate School of Biomedical Sciences; Program in Bioinformatics and Integrative Biology; Program in Molecular Medicine; Garber Lab
    Identifying the early islet cellular processes of autoimmune type 1 diabetes (T1D) in humans is challenging given the absence of symptoms during this period and the inaccessibility of the pancreas for sampling. In this article, we study temporal events in pancreatic islets in LEW.1WR1 rats, in which autoimmune diabetes can be induced with virus infection, by performing transcriptional analysis of islets harvested during the prediabetic period. Single-cell RNA-sequencing and differential expression analyses of islets from prediabetic rats reveal subsets of β- and α-cells under stress as evidenced by heightened expression, over time, of a transcriptional signature characterized by interferon-stimulated genes, chemokines including Cxcl10, major histocompatibility class I, and genes for the ubiquitin-proteasome system. Mononuclear phagocytes show increased expression of inflammatory markers. RNA-in situ hybridization of rat pancreatic tissue defines the spatial distribution of Cxcl10+ β- and α-cells and their association with CD8+ T cell infiltration, a hallmark of insulitis and islet destruction. Our studies define early islet transcriptional events during immune cell recruitment to islets and reveal spatial associations between stressed β- and α-cells and immune cells. Insights into such early processes can assist in the development of therapeutic and prevention strategies for T1D.
  • Publication
    Intratracheally administered LNA gapmer antisense oligonucleotides induce robust gene silencing in mouse lung fibroblasts
    (2022-08-03) Shin, Minwook; Chan, Io Long; Cao, Yuming; Gruntman, Alisha M; Lee, Jonathan; Sousa, Jacquelyn; Rodríguez, Tomás C; Echeverria, Dimas; Devi, Gitali; Debacker, Alexandre J; Moazami, Michael P; Krishnamurthy, Pranathi Meda; Rembetsy-Brown, Julia M; Kelly, Karen; Yukselen, Onur; Donnard, Elisa; Parsons, Teagan J; Khvorova, Anastasia; Sontheimer, Erik J; Maehr, René; Garber, Manuel; Watts, Jonathan K; Biochemistry and Molecular Biotechnology; Diabetes Center of Excellence; Horae Gene Therapy Center; Li Weibo Institute for Rare Diseases Research; Morningside Graduate School of Biomedical Sciences; Pediatrics; Program in Bioinformatics and Integrative Biology; Program in Molecular Medicine; RNA Therapeutics Institute
    The lung is a complex organ with various cell types having distinct roles. Antisense oligonucleotides (ASOs) have been studied in the lung, but it has been challenging to determine their effectiveness in each cell type due to the lack of appropriate analytical methods. We employed three distinct approaches to study silencing efficacy within different cell types. First, we used lineage markers to identify cell types in flow cytometry, and simultaneously measured ASO-induced silencing of cell-surface proteins CD47 or CD98. Second, we applied single-cell RNA sequencing (scRNA-seq) to measure silencing efficacy in distinct cell types; to the best of our knowledge, this is the first time scRNA-seq has been applied to measure the efficacy of oligonucleotide therapeutics. In both approaches, fibroblasts were the most susceptible to locally delivered ASOs, with significant silencing also in endothelial cells. Third, we confirmed that the robust silencing in fibroblasts is broadly applicable by silencing two targets expressed mainly in fibroblasts, Mfap4 and Adam33. Across independent approaches, we demonstrate that intratracheally administered LNA gapmer ASOs robustly induce gene silencing in lung fibroblasts. ASO-induced gene silencing in fibroblasts was durable, lasting 4-8 weeks after a single dose. Thus, lung fibroblasts are well aligned with ASOs as therapeutics.
  • Publication
    The Bioinformatics Core and The Garber Lab
    (2012-11-29) Garber, Manuel
    Dr. Manuel Garber discusses the services and educational programs that are offered through the new Bioinformatics Core.
  • Publication
    Genetic and Epigenetic Variation, but Not Diet, Shape the Sperm Methylome
    (2015-12-21) Shea, Jeremy; Serra, Ryan W.; Carone, Benjamin R.; Shulha, Hennady P.; Kucukural, Alper; Ziller, Michael; Vallaster, Markus; Gu, Hongcang; Tapper, Andrew R.; Gardner, Paul D.; Meissner, Alexander; Garber, Manuel; Rando, Oliver J.; Gardner Lab; Tapper Lab; Department of Psychiatry; Brudnick Neuropsychiatric Research Institute; Bioinformatics Core; Program in Bioinformatics and Integrative Biology; Department of Biochemistry and Molecular Pharmacology
    Paternal diet can impact metabolic phenotypes in offspring, but mechanisms underlying such intergenerational information transfer remain obscure. Here, we interrogate cytosine methylation patterns in sperm obtained from mice consuming one of three diets, generating whole genome methylation maps for four pools of sperm samples and for 12 individual sperm samples, as well as 61 genome-scale methylation maps. We find that "epivariation," either stochastic or due to unknown demographic or environmental factors, was a far stronger contributor to the sperm methylome than was the diet consumed. Variation in cytosine methylation was particularly dramatic over tandem repeat families, including ribosomal DNA (rDNA) repeats, but rDNA methylation was strongly correlated with genetic variation in rDNA copy number and was not influenced by paternal diet. These results identify loci of genetic and epigenetic lability in the mammalian genome but argue against a direct role for sperm cytosine methylation in dietary reprogramming of offspring metabolism.
  • Publication
    Biogenesis and function of tRNA fragments during sperm maturation and fertilization in mammals
    (2016-01-22) Sharma, Upasna; Conine, Colin C.; Shea, Jeremy; Boskovic, Ana; Derr, Alan G.; Bing, Xin Y.; Belleannee, Clemence; Kucukural, Alper; Serra, Ryan W.; Sun, Fengyun; Song, Lina; Carone, Benjamin R.; Ricci, Emiliano P.; Li, Xin Z.; Fauquier, Lucas; Moore, Melissa J.; Sullivan, Robert; Mello, Craig C.; Garber, Manuel; Rando, Oliver J.; RNAi Therapeutics Institute; Program in Bioinformatics and Integrative Biology; Program in Molecular Medicine; Department of Biochemistry and Molecular Pharmacology
    Several recent studies link parental environments to phenotypes in subsequent generations. In this work, we investigate the mechanism by which paternal diet affects offspring metabolism. Protein restriction in mice affects small RNA (sRNA) levels in mature sperm, with decreased let-7 levels and increased amounts of 5' fragments of glycine transfer RNAs (tRNAs). In testicular sperm, tRNA fragments are scarce but increase in abundance as sperm mature in the epididymis. Epididymosomes (vesicles that fuse with sperm during epididymal transit) carry RNA payloads matching those of mature sperm and can deliver RNAs to immature sperm in vitro. Functionally, tRNA-glycine-GCC fragments repress genes associated with the endogenous retroelement MERVL, in both embryonic stem cells and embryos. Our results shed light on sRNA biogenesis and its dietary regulation during posttesticular sperm maturation, and they also link tRNA fragments to regulation of endogenous retroelements active in the preimplantation embryo.
  • Publication
    Evolutionary dynamics and tissue specificity of human long noncoding RNAs in six mammals
    (2014-04-01) Washietl, Stefan; Kellis, Manolis; Garber, Manuel; Program in Bioinformatics and Integrative Biology; Program in Molecular Medicine
    Long intergenic noncoding RNAs (lincRNAs) play diverse regulatory roles in human development and disease, but little is known about their evolutionary history and constraint. Here, we characterize human lincRNA expression patterns in nine tissues across six mammalian species and multiple individuals. Of the 1898 human lincRNAs expressed in these tissues, we find orthologous transcripts for 80% in chimpanzee, 63% in rhesus, 39% in cow, 38% in mouse, and 35% in rat. Mammalian-expressed lincRNAs show remarkably strong conservation of tissue specificity, suggesting that it is selectively maintained. In contrast, abundant splice-site turnover suggests that exact splice sites are not critical. Relative to evolutionarily young lincRNAs, mammalian-expressed lincRNAs show higher primary sequence conservation in their promoters and exons, increased proximity to protein-coding genes enriched for tissue-specific functions, fewer repeat elements, and more frequent single-exon transcripts. Remarkably, we find that approximately 20% of human lincRNAs are not expressed beyond chimpanzee and are undetectable even in rhesus. These hominid-specific lincRNAs are more tissue specific, enriched for testis, and faster evolving within the human lineage.
  • Publication
    Ebola Virus Glycoprotein with Increased Infectivity Dominated the 2013-2016 Epidemic
    (2016-11-03) Diehl, William E; Kim, Kyusik; Kyawe, Pyae Phyo; McCauley, Sean M.; Donnard, Elisa; Kucukural, Alper; McDonel, Patrick E.; Garber, Manuel; Luban, Jeremy; Department of Medicine; Program in Molecular Medicine
    The magnitude of the 2013-2016 Ebola virus disease (EVD) epidemic enabled an unprecedented number of viral mutations to occur over successive human-to-human transmission events, increasing the probability that adaptation to the human host occurred during the outbreak. We investigated one nonsynonymous mutation, Ebola virus (EBOV) glycoprotein (GP) mutant A82V, for its effect on viral infectivity. This mutation, located at the NPC1-binding site on EBOV GP, occurred early in the 2013-2016 outbreak and rose to high frequency. We found that GP-A82V had heightened ability to infect primate cells, including human dendritic cells. The increased infectivity was restricted to cells that have primate-specific NPC1 sequences at the EBOV interface, suggesting that this mutation was indeed an adaptation to the human host. GP-A82V was associated with increased mortality, consistent with the hypothesis that the heightened intrinsic infectivity of GP-A82V contributed to disease severity during the EVD epidemic.
  • Publication
    Defining the 5 and 3 landscape of the Drosophila transcriptome with Exo-seq and RNaseH-seq
    (2017-02-22) Afik, Shaked; Bartok, Osnat; Artyomov, Maxim N.; Shishkin, Alexander A.; Kadri, Sabah; Hanan, Mor; Zhu, Xiaopeng; Garber, Manuel; Kadener, Sebastian; Program in Bioinformatics and Integrative Biology
    Cells regulate biological responses in part through changes in transcription start sites (TSS) or cleavage and polyadenylation sites (PAS). To fully understand gene regulatory networks, it is therefore critical to accurately annotate cell type-specific TSS and PAS. Here we present a simple and straightforward approach for genome-wide annotation of 5- and 3-RNA ends. Our approach reliably discerns bona fide PAS from false PAS that arise due to internal poly(A) tracts, a common problem with current PAS annotation methods. We applied our methodology to study the impact of temperature on the Drosophila melanogaster head transcriptome. We found hundreds of previously unidentified TSS and PAS which revealed two interesting phenomena: first, genes with multiple PASs tend to harbor a motif near the most proximal PAS, which likely represents a new cleavage and polyadenylation signal. Second, motif analysis of promoters of genes affected by temperature suggested that boundary element association factor of 32 kDa (BEAF-32) and DREF mediates a transcriptional program at warm temperatures, a result we validated in a fly line where beaf-32 is downregulated. These results demonstrate the utility of a high-throughput platform for complete experimental and computational analysis of mRNA-ends to improve gene annotation.
  • Publication
    Comparative Analysis of Immune Cells Reveals a Conserved Regulatory Lexicon
    (2018-03-28) Donnard, Elisa; Vangala, Pranitha; Afik, Shaked; McCauley, Sean M.; Nowosielska, Anetta; Kucukural, Alper; Tabak, Barbara; Zhu, Xiaopeng; Diehl, William E; McDonel, Patrick; Yosef, Nir; Luban, Jeremy; Garber, Manuel; Garber Lab; Bioinformatics Core; Program in Molecular Medicine; Program in Bioinformatics and Integrative Biology
    Most well-characterized enhancers are deeply conserved. In contrast, genome-wide comparative studies of steady-state systems showed that only a small fraction of active enhancers are conserved. To better understand conservation of enhancer activity, we used a comparative genomics approach that integrates temporal expression and epigenetic profiles in an innate immune system. We found that gene expression programs diverge among mildly induced genes, while being highly conserved for strongly induced genes. The fraction of conserved enhancers varies greatly across gene expression programs, with induced genes and early-response genes, in particular, being regulated by a higher fraction of conserved enhancers. Clustering of conserved accessible DNA sequences within enhancers resulted in over 60 sequence motifs including motifs for known factors, as well as many with unknown function. We further show that the number of instances of these motifs is a strong predictor of the responsiveness of a gene to pathogen detection.
  • Publication
    End Sequence Analysis Toolkit (ESAT) expands the extractable information from single-cell RNA-seq data
    (2016-10-01) Derr, Alan G.; Yang, Chaoxing; Zilionis, Rapolas; Sergushichev, Alexey; Blodgett, David; Redick, Sambra D.; Bortell, Rita; Luban, Jeremy; Harlan, David M.; Kadener, Sebastian; Greiner, Dale L.; Klein, Allon; Artyomov, Maxim N.; Garber, Manuel; Department of Medicine; Program in Molecular Medicine, Diabetes Center of Excellence; Program in Bioinformatics and Integrative Biology
    RNA-seq protocols that focus on transcript termini are well suited for applications in which template quantity is limiting. Here we show that, when applied to end-sequencing data, analytical methods designed for global RNA-seq produce computational artifacts. To remedy this, we created the End Sequence Analysis Toolkit (ESAT). As a test, we first compared end-sequencing and bulk RNA-seq using RNA from dendritic cells stimulated with lipopolysaccharide (LPS). As predicted by the telescripting model for transcriptional bursts, ESAT detected an LPS-stimulated shift to shorter 3'-isoforms that was not evident by conventional computational methods. Then, droplet-based microfluidics was used to generate 1000 cDNA libraries, each from an individual pancreatic islet cell. ESAT identified nine distinct cell types, three distinct beta-cell types, and a complex interplay between hormone secretion and vascularization. ESAT, then, offers a much-needed and generally applicable computational pipeline for either bulk or single-cell RNA end-sequencing.
  • Publication
    Epstein-barr virus latent membrane protein 1 genetic variability in peripheral blood B cells and oropharyngeal fluids
    (2014-04-01) Renzette, Nicholas; Somasundaran, Mohan; Brewster, Frank E.; Coderre, James; Weiss, Eric R.; McManus, Margaret M.; Greenough, Thomas C.; Tabak, Barbara; Garber, Manuel; Kowalik, Timothy F.; Ruiz De Luzuriaga, Katherine; Department of Bioinformatics and Integrative Biology; Progam in Molecular Medicine; Department of Pediatrics; Department of Microbiology and Physiological Systems
    We report the diversity of latent membrane protein 1 (LMP1) gene founder sequences and the level of Epstein-Barr virus (EBV) genome variability over time and across anatomic compartments by using virus genomes amplified directly from oropharyngeal wash specimens and peripheral blood B cells during acute infection and convalescence. The intrahost nucleotide variability of the founder virus was 0.02% across the region sequences, and diversity increased significantly over time in the oropharyngeal compartment (P = 0.004). The LMP1 region showing the greatest level of variability in both compartments, and over time, was concentrated within the functional carboxyl-terminal activating regions 2 and 3 (CTAR2 and CTAR3). Interestingly, a deletion in a proline-rich repeat region (amino acids 274 to 289) of EBV commonly reported in EBV sequenced from cancer specimens was not observed in acute infectious mononucleosis (AIM) patients. Taken together, these data highlight the diversity in circulating EBV genomes and its potential importance in disease pathogenesis and vaccine design. IMPORTANCE: This study is among the first to leverage an improved high-throughput deep-sequencing methodology to investigate directly from patient samples the degree of diversity in Epstein-Barr virus (EBV) populations and the extent to which viral genome diversity develops over time in the infected host. Significant variability of circulating EBV latent membrane protein 1 (LMP1) gene sequences was observed between cellular and oral wash samples, and this variability increased over time in oral wash samples. The significance of EBV genetic diversity in transmission and disease pathogenesis are discussed.
  • Publication
    Recovery of viable endocrine-specific cells and transcriptomes from human pancreatic islet-engrafted mice
    (2020-01-01) Redick, Sambra D.; Leehy, Linda; Rittenhouse, Ann R.; Blodgett, David M.; Derr, Alan G.; Kucukural, Alper; Garber, Manuel; Shultz, Leonard D.; Greiner, Dale L.; Wang, Jennifer P.; Harlan, David M.; Bortell, Rita; Jurczyk, Agata; Garber Lab; Program in Bioinformatics and Integrative Biology; Department of Medicine; Department of Microbiology and Physiological Systems; Program in Molecular Medicine; Diabetes Center of Excellence
    Human pancreatic islets engrafted into immunodeficient mice serve as an important model for in vivo human diabetes studies. Following engraftment, islet function can be monitored in vivo by measuring circulating glucose and human insulin; however, it will be important to recover viable cells for more complex graft analyses. Moreover, RNA analyses of dissected grafts have not distinguished which hormone-specific cell types contribute to gene expression. We developed a method for recovering live cells suitable for fluorescence-activated cell sorting from human islets engrafted in mice. Although yields of recovered islet cells were relatively low, the ratios of bulk-sorted beta, alpha, and delta cells and their respective hormone-specific RNA-Seq transcriptomes are comparable pretransplant and posttransplant, suggesting that the cellular characteristics of islet grafts posttransplant closely mirror the original donor islets. Single-cell RNA-Seq transcriptome analysis confirms the presence of appropriate beta, alpha, and delta cell subsets. In addition, ex vivo perifusion of recovered human islet grafts demonstrated glucose-stimulated insulin secretion. Viable cells suitable for patch-clamp analysis were recovered from transplanted human embryonic stem cell-derived beta cells. Together, our functional and hormone-specific transcriptome analyses document the broad applicability of this system for longitudinal examination of human islet cells undergoing developmental/metabolic/pharmacogenetic manipulation in vivo and may facilitate the discovery of treatments for diabetes.
  • Publication
    A comparative genomics multitool for scientific discovery and conservation
    (Nature Publishing Group, 2020-11-11) Zoonomia Consortium; Genereux, Diane P.; Garber, Manuel; Lindblad-Toh, Kerstin; Karlsson, Elinor K; Program in Molecular Medicine; Garber Lab; Program in Bioinformatics and Integrative Biology
    The Zoonomia Project is investigating the genomics of shared and specialized traits in eutherian mammals. Here we provide genome assemblies for 131 species, of which all but 9 are previously uncharacterized, and describe a whole-genome alignment of 240 species of considerable phylogenetic diversity, comprising representatives from more than 80% of mammalian families. We find that regions of reduced genetic diversity are more abundant in species at a high risk of extinction, discern signals of evolutionary selection at high resolution and provide insights from individual reference genomes. By prioritizing phylogenetic diversity and making data available quickly and without restriction, the Zoonomia Project aims to support biological discovery, medical research and the conservation of biodiversity.
  • Publication
    DolphinNext: a distributed data processing platform for high throughput genomics
    (2020-04-19) Yukselen, Onur; Turkyilmaz, Osman; Ozturk, Ahmet R.; Garber, Manuel; Kucukural, Alper; Garber Lab; Program in Bioinformatics and Integrative Biology; Program in Molecular Medicine; RNA Therapeutics Institute; Bioinformatics Core
    BACKGROUND: The emergence of high throughput technologies that produce vast amounts of genomic data, such as next-generation sequencing (NGS) is transforming biological research. The dramatic increase in the volume of data, the variety and continuous change of data processing tools, algorithms and databases make analysis the main bottleneck for scientific discovery. The processing of high throughput datasets typically involves many different computational programs, each of which performs a specific step in a pipeline. Given the wide range of applications and organizational infrastructures, there is a great need for highly parallel, flexible, portable, and reproducible data processing frameworks. Several platforms currently exist for the design and execution of complex pipelines. Unfortunately, current platforms lack the necessary combination of parallelism, portability, flexibility and/or reproducibility that are required by the current research environment. To address these shortcomings, workflow frameworks that provide a platform to develop and share portable pipelines have recently arisen. We complement these new platforms by providing a graphical user interface to create, maintain, and execute complex pipelines. Such a platform will simplify robust and reproducible workflow creation for non-technical users as well as provide a robust platform to maintain pipelines for large organizations. RESULTS: To simplify development, maintenance, and execution of complex pipelines we created DolphinNext. DolphinNext facilitates building and deployment of complex pipelines using a modular approach implemented in a graphical interface that relies on the powerful Nextflow workflow framework by providing 1. A drag and drop user interface that visualizes pipelines and allows users to create pipelines without familiarity in underlying programming languages. 2. Modules to execute and monitor pipelines in distributed computing environments such as high-performance clusters and/or cloud 3. Reproducible pipelines with version tracking and stand-alone versions that can be run independently. 4. Modular process design with process revisioning support to increase reusability and pipeline development efficiency. 5. Pipeline sharing with GitHub and automated testing 6. Extensive reports with R-markdown and shiny support for interactive data visualization and analysis. CONCLUSION: DolphinNext is a flexible, intuitive, web-based data processing and analysis platform that enables creating, deploying, sharing, and executing complex Nextflow pipelines with extensive revisioning and interactive reporting to enhance reproducible results.
  • Publication
    Diverse repertoire of human adipocyte subtypes develops from transcriptionally distinct mesenchymal progenitor cells
    (2019-09-03) Min, So Yun; Desai, Anand; Yang, Zinger; Sharma, Agastya; DeSouza, Tiffany; Genga, Ryan; Kucukural, Alper; Lifshitz, Lawrence M.; Nielsen, Soren; Scheele, Camilla; Maehr, Rene; Garber, Manuel; Corvera, Silvia; Garber Lab; Program in Bioinformatics and Integrative Biology; Department of Medicine, Diabetes Center of Excellence; Morningside Graduate School of Biomedical Sciences; Program in Molecular Medicine
    Single-cell sequencing technologies have revealed an unexpectedly broad repertoire of cells required to mediate complex functions in multicellular organisms. Despite the multiple roles of adipose tissue in maintaining systemic metabolic homeostasis, adipocytes are thought to be largely homogenous with only 2 major subtypes recognized in humans so far. Here we report the existence and characteristics of 4 distinct human adipocyte subtypes, and of their respective mesenchymal progenitors. The phenotypes of these distinct adipocyte subtypes are differentially associated with key adipose tissue functions, including thermogenesis, lipid storage, and adipokine secretion. The transcriptomic signature of "brite/beige" thermogenic adipocytes reveals mechanisms for iron accumulation and protection from oxidative stress, necessary for mitochondrial biogenesis and respiration upon activation. Importantly, this signature is enriched in human supraclavicular adipose tissue, confirming that these cells comprise thermogenic depots in vivo, and explain previous findings of a rate-limiting role of iron in adipose tissue browning. The mesenchymal progenitors that give rise to beige/brite adipocytes express a unique set of cytokines and transcriptional regulators involved in immune cell modulation of adipose tissue browning. Unexpectedly, we also find adipocyte subtypes specialized for high-level expression of the adipokines adiponectin or leptin, associated with distinct transcription factors previously implicated in adipocyte differentiation. The finding of a broad adipocyte repertoire derived from a distinct set of mesenchymal progenitors, and of the transcriptional regulators that can control their development, provides a framework for understanding human adipose tissue function and role in metabolic disease.
  • Publication
    DNA-binding-domain fusions enhance the targeting range and precision of Cas9
    (2015-12-01) Bolukbasi, Mehmet Fatih; Gupta, Ankit; Oikemus, Sarah; Derr, Alan G.; Garber, Manuel; Brodsky, Michael H.; Zhu, Lihua Julie; Wolfe, Scot A.; Program in Molecular Medicine; Program in Bioinformatics and Integrative Biology; Department of Biochemistry and Molecular Pharmacology; Department of Molecular, Cell and Cancer Biology
    The CRISPR-Cas9 system is commonly used in biomedical research; however, the precision of Cas9 is suboptimal for applications that involve editing a large population of cells (for example, gene therapy). Variations on the standard Cas9 system have yielded improvements in the precision of targeted DNA cleavage, but they often restrict the range of targetable sequences. It remains unclear whether these variants can limit lesions to a single site in the human genome over a large cohort of treated cells. Here we show that by fusing a programmable DNA-binding domain (pDBD) to Cas9 and attenuating Cas9's inherent DNA-binding affinity, we were able to produce a Cas9-pDBD chimera with dramatically improved precision and an increased targeting range. Because the specificity and affinity of this framework can be easily tuned, Cas9-pDBDs provide a flexible system that can be tailored to achieve extremely precise genome editing at nearly any genomic locus.
  • Publication
    Transcriptome-wide Analysis of Roles for tRNA Modifications in Translational Regulation
    (2017-12-07) Chou, Hsin-Jung; Donnard, Elisa; Gustafsson, H. Tobias; Garber, Manuel; Rando, Oliver J.; Garber Lab; Program in Molecular Medicine; Program in Bioinformatics and Integrative Biology; Department of Biochemistry and Molecular Pharmacology
    Covalent nucleotide modifications in noncoding RNAs affect a plethora of biological processes, and new functions continue to be discovered even for well-known modifying enzymes. To systematically compare the functions of a large set of noncoding RNA modifications in gene regulation, we carried out ribosome profiling in budding yeast to characterize 57 nonessential genes involved in tRNA modification. Deletion mutants exhibited a range of translational phenotypes, with enzymes known to modify anticodons, or non-tRNA substrates such as rRNA, exhibiting the most dramatic translational perturbations. Our data build on prior reports documenting translational upregulation of the nutrient-responsive transcription factor Gcn4 in response to numerous tRNA perturbations, and identify many additional translationally regulated mRNAs throughout the yeast genome. Our data also uncover unexpected roles for tRNA-modifying enzymes in regulation of TY retroelements, and in rRNA 2'-O-methylation. This dataset should provide a rich resource for discovery of additional links between tRNA modifications and gene regulation.
  • Publication
    A negative feedback loop of transcription factors specifies alternative dendritic cell chromatin States
    (2014-12-18) Bornstein, Chamutal; Winter, Deborah; Barnett-Itzhaki, Zohar; David, Eyal; Kadri, Sabah; Garber, Manuel; Amit, Ido; Garber Lab; Program in Bioinformatics and Integrative Biology
    During hematopoiesis, cells originating from the same stem cell reservoir differentiate into distinct cell types. The mechanisms enabling common progenitors to differentiate into alternative cell fates are not fully understood. Here, we identify cell-fate-determining transcription factors (TFs) governing dendritic cell (DC) development by annotating the enhancer landscapes of the DC lineage. Combining these analyses with detailed overexpression, knockdown, and ChIP-Seq studies, we show that Irf8 functions as a plasmacytoid DC epigenetic and fate-determining TF, regulating massive, cell-specific chromatin changes in thousands of pDC enhancers. Importantly, Irf8 forms a negative feedback loop with Cebpb, a monocyte-derived DC epigenetic fate-determining TF. We show that using this circuit logic, a pulse of TF expression can stably define epigenetic and transcriptional states, regardless of the microenvironment. More broadly, our study proposes a general paradigm that allows closely related cells with a similar set of signal-dependent factors to generate differential and persistent enhancer landscapes.