Search Our Scientific Publications & Authors

Genome Biol 2021 Apr 16;22(1):110. Epub 2021 Apr 16.

Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, Berlin, Germany.

Background: X-chromosomal genes contribute to sex differences, in particular during early development, when both X chromosomes are active in females. Double X-dosage shifts female pluripotent cells towards the naive stem cell state by increasing pluripotency factor expression, inhibiting the differentiation-promoting MAP kinase (MAPK) signaling pathway, and delaying differentiation.

Results: To identify the genetic basis of these sex differences, we use a two-step CRISPR screening approach to comprehensively identify X-linked genes that cause the female pluripotency phenotype in murine embryonic stem cells. Read More

J Biol Chem 2021 Apr 14:100643. Epub 2021 Apr 14.

Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Morgridge Institute for Research, Madison, WI 53715, USA; National Center for Quantitative Biology of Complex Systems, Madison, WI 53562, USA; Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, Missouri 63110, USA; Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, USA; Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA. Electronic address:

Coenzyme Q (CoQ), a redox-active lipid essential for oxidative phosphorylation, is synthesized by virtually all cells, but how eukaryotes make the universal CoQ head group precursor 4-hydroxybenzoate (4-HB) from tyrosine is unknown. The first and last steps of this pathway have been defined in Saccharomyces cerevisiae, but the intermediates and enzymes involved in converting 4-hydroxyphenylpyruvate (4-HPP) to 4-hydroxybenzaldehyde (4-HBz) have not been described. Here, we interrogate this pathway with genetic screens, targeted LC-MS, and chemical genetics. Read More

Addiction 2021 Apr 16. Epub 2021 Apr 16.

Yale University School of Public Health, New Haven, CT, USA.

Background And Aims: The Alcohol Use Disorders Identification Test-Consumption (AUDIT-C) questionnaire screens for harmful drinking using a 12-month timeframe. A score of 0 is assigned to individuals who report abstaining from alcohol in the past year. However, many middle-aged individuals reporting current abstinence are former drinkers (FDs). Read More

Mucosal Immunol 2021 Apr 15. Epub 2021 Apr 15.

Université de Paris, Imagine Institute, Laboratory of Intestinal Immunity, INSERM UMR 1163, Paris, France.

The mechanisms that maintain intestinal homeostasis despite constant exposure of the gut surface to multiple environmental antigens and to billions of microbes have been scrutinized over the past 20 years with the goals to gain basic knowledge, but also to elucidate the pathogenesis of inflammatory bowel diseases (IBD) and to identify therapeutic targets for these severe diseases. Considerable insight has been obtained from studies based on gene inactivation in mice as well as from genome wide screens for genetic variants predisposing to human IBD. These studies are, however, not sufficient to delineate which pathways play key nonredundant role in the human intestinal barrier and to hierarchize their respective contribution. Read More

MicroPubl Biol 2021 Apr 8;2021. Epub 2021 Apr 8.

Biology Department, University of Detroit Mercy, Detroit, MI USA.

Genetic screens provide a mechanism to identify genes involved with different cellular and organismal processes. Using a Flp/FRT screen in the eye we identified mutations that result in alterations and de-regulation of cell growth and division. From this screen a group of undergraduate researchers part of the Fly-CURE consortium mapped and characterized a new allele of the gene , Read More

Cancer Cell 2021 Apr;39(4):566-579.e7

Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institute of Health, Rockville, MD 20850, USA; Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.

Small cell neuroendocrine cancers (SCNCs) are recalcitrant cancers arising from diverse primary sites that lack effective treatments. Using chemical genetic screens, we identified inhibition of ataxia telangiectasia and rad3 related (ATR), the primary activator of the replication stress response, and topoisomerase I (TOP1), nuclear enzyme that suppresses genomic instability, as synergistically cytotoxic in small cell lung cancer (SCLC). In a proof-of-concept study, we combined M6620 (berzosertib), first-in-class ATR inhibitor, and TOP1 inhibitor topotecan in patients with relapsed SCNCs. Read More

Methods Mol Biol 2021 ;2307:123-137

Chemical and Environmental Engineering, University of California Riverside, Riverside, CA, USA.

Genome-wide functional genomic screens are essential to determining the genetic underpinning of a biological process. Novel and powerful tools for perturbing gene function, with the help of genetic and epigenetic information, have made it possible to systematically investigate the contribution of every gene to evolved and engineered phenotypes. Functional genomics and screening for enhanced phenotypes become ever more important when dealing with nonconventional hosts. Read More

Oncogene 2021 Apr 12. Epub 2021 Apr 12.

Medical Research Center, Genomic Medicine Institute, Seoul National University College of Medicine, Seoul, Korea.

Metastatic or recurrent colorectal cancer (CRC) patients require systemic chemotherapy, but the therapeutic options of targeted agents remain limited. CRC patients with KRAS or BRAF gene mutations exhibit a worse prognosis and are resistant to anti-EGFR treatment. Previous studies have shown that the expression of anti-apoptotic protein BCL-X is increased in CRC patients with KRAS/BRAF mutations, suggesting BCL-X as a therapeutic target for this subgroup. Read More

Hered Cancer Clin Pract 2021 Apr 9;19(1):24. Epub 2021 Apr 9.

Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre and Royal Melbourne Hospital, Melbourne, Australia.

Background: This nationwide study assessed the impact of nationally agreed cancer genetics guidelines on use of BRCA1/2 germline testing, risk management advice given by health professionals to women with pathogenic BRCA1/2 variants and uptake of such advice by patients.

Methods: Clinic files of 883 women who had initial proband screens for BRCA1/2 pathogenic variants at 12 familial cancer clinics between July 2008-July 2009 (i.e. Read More

Trends Immunol 2021 Mar 31. Epub 2021 Mar 31.

Program in Immunology, Stanford University School of Medicine, Stanford, CA, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA; Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA. Electronic address:

CRISPR-Cas9 technologies have transformed the study of genetic pathways governing cellular differentiation and function. Recent advances have adapted these methods to immune cells, which has accelerated the pace of functional genomics in immunology and enabled new avenues for the design of cellular immunotherapies for cancer. In this review, we summarize recent developments in CRISPR-Cas9 technology and discuss how they have been leveraged to discover and manipulate novel genetic regulators of the immune system. Read More

Pathogens 2021 Mar 16;10(3). Epub 2021 Mar 16.

Center for Global Health and Infectious Diseases Research and USF Genomics Program, College of Public Health, University of South Florida, 3720 Spectrum Blvd, Suite 404, Tampa, FL 33612, USA.

Mosquito transmission of the deadly malaria parasite is mediated by mature sexual forms (gametocytes). Circulating in the vertebrate host, relatively few intraerythrocytic gametocytes are picked up during a bloodmeal to continue sexual development in the mosquito vector. Human-to-vector transmission thus represents an infection bottleneck in the parasite's life cycle for therapeutic interventions to prevent malaria. Read More

Cancers (Basel) 2021 Mar 30;13(7). Epub 2021 Mar 30.

Genome Instability and DNA Repair Syndromes Group, Sant Pau Biomedical Research Institute (IIB Sant Pau) and Join Unit UAB-IR Sant Pau on Genomic Medicine, 08041 Barcelona, Spain.

Cancer is a complex disease resulting from the accumulation of genetic dysfunctions. Tumor heterogeneity causes the molecular variety that divergently controls responses to chemotherapy, leading to the recurrent problem of cancer reappearance. For many decades, efforts have focused on identifying essential tumoral genes and cancer driver mutations. Read More

Viruses 2021 Mar 10;13(3). Epub 2021 Mar 10.

Department of Global Health, University of Washington, Seattle, WA 98109, USA.

The concerning increase in HIV-1 resistance argues for prioritizing the development of host-targeting antiviral drugs because such drugs can offer high genetic barriers to the selection of drug-resistant viral variants. Targeting host proteins could also yield drugs that act on viral life cycle events that have proven elusive to inhibition, such as intracellular events of HIV-1 immature capsid assembly. Here, we review small molecule inhibitors identified primarily through HIV-1 self-assembly screens and describe how all act either narrowly post-entry or broadly on early and late events of the HIV-1 life cycle. Read More

Int J Mol Sci 2021 Mar 27;22(7). Epub 2021 Mar 27.

Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011, USA.

Forward genetic screens have shown the consequences of deleterious mutations; however, they are best suited for model organisms with fast reproductive rates and large broods. Furthermore, investigators must faithfully identify changes in phenotype, even if subtle, to realize the full benefit of the screen. Reverse genetic approaches also probe genotype to phenotype relationships, except that the genetic targets are predefined. Read More

Int J Mol Sci 2021 Mar 8;22(5). Epub 2021 Mar 8.

Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ 08854, USA.

Plants in the family Lemnaceae are aquatic monocots and the smallest, simplest, and fastest growing angiosperms. Their small size, the smallest family member is 0.5 mm and the largest is 2. Read More

Int J Mol Sci 2021 Mar 8;22(5). Epub 2021 Mar 8.

Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA.

The fruit fly, , has been used to understand fundamental principles of genetics and biology for over a century. is now also considered an essential tool to study mechanisms underlying numerous human genetic diseases. In this review, we will discuss how flies can be used to deepen our knowledge of infectious disease mechanisms in vivo. Read More

Nat Commun 2021 04 1;12(1):2032. Epub 2021 Apr 1.

Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada.

Adherent-invasive Escherichia coli (AIEC) are pathogenic bacteria frequently isolated from patients who have Crohn's disease (CD). Despite the phenotypic differences between AIEC and commensal E. coli, comparative genomic approaches have been unable to differentiate these two groups, making the identification of key virulence factors a challenge. Read More

Blood Adv 2021 Apr;5(7):1862-1875

Institute for Molecular Medicine Finland, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland.

Mature natural killer (NK) cell neoplasms are rare but very aggressive types of cancers. With currently available treatments, they have a very poor prognosis and, as such, are an example of group of cancers in which the development of effective precision therapies is needed. Using both short- and long-term drug sensitivity testing, we explored novel ways to target NK-cell neoplasms by combining the clinically approved JAK inhibitor ruxolitinib with other targeted agents. Read More

Cold Spring Harb Protoc 2021 Mar 30. Epub 2021 Mar 30.

The Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, United Kingdom

is one of the premier model systems to study cell and developmental biology in vivo in vertebrates. Here we briefly review how this South African frog came to be favored by a large community of scientists after the explosive growth of molecular biology and examine some of the original discoveries arising from this sturdy frog. Experimental embryology started in but developed in newt embryos for historical reasons. Read More

Cancer Sci 2021 Mar 30. Epub 2021 Mar 30.

Genetics Department, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.

Cancer genome sequencing studies have identified driver genes for a variety of different cancers and helped to understand the genetic landscape of human cancer. It is still challenging, however, to identify cancer driver genes with confidence simply from genetic data alone. In vivo forward genetic screens using Sleeping Beauty (SB) transposon mutagenesis provides another powerful genetic tool for identifying candidate cancer driver genes in wild type and sensitized mouse tumors. Read More

Brief Funct Genomics 2021 Mar 30. Epub 2021 Mar 30.

Cell competition is defined as the context-dependent elimination of cells that is mediated by intercellular communication, such as paracrine or contact-dependent cell signaling, and/or mechanical stresses. It is considered to be a quality control mechanism that facilitates the removal of suboptimal cells from both adult and embryonic tissues. Cell competition, however, can also be hijacked by transformed cells to acquire a 'super-competitor' status and outcompete the normal epithelium to establish a precancerous field. Read More

Proc Natl Acad Sci U S A 2021 Apr;118(14)

Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada

Genetic screens can identify synthetic lethal (SL) interactions and uncover potential anticancer therapeutic targets. However, most SL screens have utilized knockout or knockdown approaches that do not accurately mimic chemical inhibition of a target protein. Here, we test whether missense mutations can be utilized as a model for a type of protein inhibition that creates a dominant gain-of-function cytotoxicity. Read More

Dev Biol 2021 Mar 25;476:68-78. Epub 2021 Mar 25.

Department of Biology, Integrated Sciences Complex, University of Massachusetts Boston, Boston, USA. Electronic address:

Vitamin A deficiency can cause human pathologies that range from blindness to embryonic malformations. This diversity is due to the lack of two major vitamin A metabolites with very different functions: the chromophore 11-cis-retinal (vitamin A aldehyde) is a critical component of the visual pigment that mediates phototransduction, while the signaling molecule all-trans-retinoic acid regulates the development of various tissues and is required for the function of the immune system. Since animals cannot synthesize vitamin A de novo, they must obtain it either as preformed vitamin A from animal products or as carotenoid precursors from plant sources. Read More

Trends Parasitol 2021 May 24;37(5):367-369. Epub 2021 Mar 24.

Laboratório de Biologia Molecular de Patógenos (LBMP), Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de São Paulo (UNIFESP), São Paulo, SP, Brazil.

Our understanding of regulatory factors in Leishmania differentiation has long been restricted by the available genetic tools, but the availability of CRISPR/Cas9 has changed the landscape forever. Recently, Baker and Catta-Preta et al. applied Cas9 editing and kinome-wide bar-seq to dissect the function of 204 kinases in the Leishmania mexicana life cycle. Read More

Genet Med 2021 Mar 26. Epub 2021 Mar 26.

Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children's Hospital, and Department of Pediatrics, Harvard Medical School, Boston, MA, USA.

Purpose: Newborn screening (NBS) is performed to identify neonates at risk for actionable, severe, early-onset disorders, many of which are genetic. The BabySeq Project randomized neonates to receive conventional NBS or NBS plus exome sequencing (ES) capable of detecting sequence variants that may also diagnose monogenic disease or indicate genetic disease risk. We therefore evaluated how ES and conventional NBS results differ in this population. Read More

Arthritis Rheumatol 2021 Mar 24. Epub 2021 Mar 24.

Biosciences Institute, Newcastle University, International Centre for Life, Newcastle upon Tyne, NE1 3BZ, United Kingdom.

Objective: Osteoarthritis (OA) is an age-related disease characterised by articular cartilage degeneration. It has a large heritability and genetic screens have identified single nucleotide polymorphisms (SNPs) marking genomic risk loci. One such locus is marked by G>A SNP rs75621460, downstream of TGFB1. Read More

BMC Genomics 2021 Mar 23;22(1):205. Epub 2021 Mar 23.

Department of Molecular and Cell Biology, Berkeley, CA, 94720, USA.

Background: CRISPR/Cas9-mediated transcriptional interference (CRISPRi) enables programmable gene knock-down, yielding loss-of-function phenotypes for nearly any gene. Effective, inducible CRISPRi has been demonstrated in budding yeast, and genome-scale guide libraries enable systematic, genome-wide genetic analysis.

Results: We present a comprehensive yeast CRISPRi library, based on empirical design rules, containing 10 distinct guides for most genes. Read More

Nat Genet 2021 04 22;53(4):529-538. Epub 2021 Mar 22.

Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.

Exciting therapeutic targets are emerging from CRISPR-based screens of high mutational-burden adult cancers. A key question, however, is whether functional genomic approaches will yield new targets in pediatric cancers, known for remarkably few mutations, which often encode proteins considered challenging drug targets. To address this, we created a first-generation pediatric cancer dependency map representing 13 pediatric solid and brain tumor types. Read More

J Bacteriol 2021 Mar 22. Epub 2021 Mar 22.

Burnett School of Biomedical Sciences, University of Central Florida, Orlando, Florida, USA

By evolving strains of that hyper-resist sedimentation, we discovered an uncharacterized mechanism that bacteria can use to remain in suspension indefinitely without expending energy. This unusual phenotype was traced to the anchoring of long colanic acid polymers (CAP) that project from the cell surface. Although each characterized mutant activated this same mechanism, the genes responsible and the strengths of the phenotypes varied. Read More