DOCSLIB.ORG

Striking Heterogeneity of Somatic L1 Retrotransposition in Single Normal

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Striking Heterogeneity of Somatic L1 Retrotransposition in Single Normal Striking heterogeneity of somatic L1 retrotransposition INAUGURAL ARTICLE in single normal and cancerous gastrointestinal cells Katsumi Yamaguchia,1, Alisha O. Soaresa, Loyal A. Goffa, Anjali Talasilaa, Jungbin A. Choia, Daria Ivenitskya, Sadik Karmaa, Benjamin Brophya, Scott E. Devineb, Stephen J. Meltzerc, and Haig H. Kazazian Jr.a,1 aDepartment of Genetic Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD 21205; bInstitute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201; and cDepartment of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD 21205 This contribution is part of the special series of Inaugural Articles by members of the National Academy of Sciences elected in 2018. Contributed by Haig H. Kazazian Jr., November 1, 2020 (sent for review September 16, 2020; reviewed by Mark A. Batzer and John V. Moran) Somatic LINE-1 (L1) retrotransposition has been detected in early et al. (14) showed that L1s are mobile in certain regions of the embryos, adult brains, and the gastrointestinal (GI) tract, and brain, particularly the hippocampus of mice. Other studies of many cancers, including epithelial GI tumors. We previously found human brain, including of single cells, solidified the consensus numerous somatic L1 insertions in paired normal and GI cancerous that somatic retrotransposition of L1 occurs in the brain, but at tissues. Here, using a modified method of single-cell analysis for low levels (∼0.2 insertions per neuron) (14–19). Somatic L1 in- somatic L1 insertions, we studied adenocarcinomas of colon, pan- sertion has also been found at very low levels in human adult creas, and stomach, and found a variable number of somatic L1 colon, stomach, esophagus, and liver (20, 21), but such data are insertions in tumors of the same type from patient to patient. We lacking for other organs. detected no somatic L1 insertions in single cells of 5 of 10 tumors In contrast, the level of L1 retrotransposition varies greatly studied. In three tumors, aneuploid cells were detected by FACS. In among different types of epithelial tumors (21–31). Retro- one pancreatic tumor, there were many more L1 insertions in an- transposition also varies from patient to patient within the same euploid than in euploid tumor cells. In one gastric cancer, both tumor type: Some tumors possess many somatic L1 insertions, aneuploid and euploid cells contained large numbers of likely while others have none (24, 25). In addition, investigators have clonal insertions. However, in a second gastric cancer with aneu- “ ” ploid cells, no somatic L1 insertions were found. We suggest that reported an artifactual detection of somatic L1 insertions from GENETICS when the cellular environment is favorable to retrotransposition, both whole tissue and single-cell analysis. Chimera artifacts arise aneuploidy predisposes tumor cells to L1 insertions, and retro- either during multiple displacement amplification (MDA) or the transposition may occur at the transition from euploidy to aneu- ligation and PCR steps of library preparation (32–35). Chimeras ploidy. Seventeen percent of insertions were also present in are sequences extending from a reference or polymorphic non- normal cells, similar to findings in genomic DNA from normal tis- reference L1Hs to a downstream flanking sequence less than 5 to sues of GI tumor patients. We provide evidence that: 1) The num- 10 kb away (33). ber of L1 insertions in tumors of the same type is highly variable, Here, we used a modified method to analyze single cells from 2) most somatic L1 insertions in GI cancer tissues are absent from adenocarcinomas of the colon, pancreas, and stomach for so- normal tissues, and 3) under certain conditions, somatic L1 retro- matic L1 insertions. We found that many presumptive new in- transposition exhibits a propensity for occurring in aneuploid cells. sertions close to reference human L1s were, in fact, artifacts: They could not be validated in any cells. They were absent from somatic retrotransposition | gastrointestinal cancer | single cells genomic DNA (gDNA) of tissues and their 5′ ends could not be recovered by PCR of the 5′ flank. As others have reported, we hile protein-coding DNA sequences make up only 1.5% of found significant patient-to-patient variability in the number of Wthe human genome, remnants of transposable elements somatic L1 insertions in tumors of the same type. Among in- comprise nearly 50% (1). The 500,000 known LINE-1s (L1s), sertions detected in tumors, about 17% (10 of 59) were also one group of retrotransposons, comprise 17% of total human DNA, but nearly all are inactive, the result of ancient truncated Significance insertions and full-length insertions that previously mutated during human evolution. We humans have some 100 to 150 ac- Using a modified method, we analyzed single cells from ade- tive L1s in our genomes (2), but only a handful of these are very nocarcinomas of the colon, pancreas, and stomach and their “ ” active or hot (2, 3). They become mobile only when their DNA paired normal tissues for somatic LINE-1 retrotransposition is transcribed into RNA, and this RNA is reverse-transcribed events. We found that somatic retrotransposition varied sig- back into DNA and inserted into the genome. This process of nificantly from patient to patient with cancers of the same retrotransposition has been modeled in cell culture (4). The L1- type, as well as in different cells within a particular cancer. encoded proteins, endonuclease and reverse transcriptase, tend to act predominantly in cis on the L1 transcript that encoded Author contributions: K.Y., L.A.G., and H.H.K. designed research; K.Y., A.O.S., A.T., J.A.C., them (5–7). Paradoxically, these autonomous elements also drive D.I., S.K., B.B., and S.E.D. performed research; S.J.M. contributed new reagents/analytic tools; S.J.M. provided samples; K.Y., A.O.S., and S.E.D. analyzed data; and K.Y. and H.H.K. the insertion of nonautonomous Alus (8), SVAs (SINE-R, VNTR, wrote the paper. Alu – and )(911), processed pseudogenes (6, 7), and other small Reviewers: M.A.B., Louisiana State University; and J.V.M., University of Michigan, RNAs (12). This process of in trans retrotransposition depends Ann Arbor. upon the L1 endonuclease and reverse transcriptase encoded by the The authors declare no competing interest. L1 ORF2 protein. Published under the PNAS license. For many years, investigators believed that L1 retrotransposition 1To whom correspondence may be addressed. Email: [email protected] or hkazazi1@ occurred exclusively in germ cells and the very early human embryo, jhmi.edu. > because so many L1s and Alus (together, 1.5 million) are fixed This article contains supporting information online at https://www.pnas.org/lookup/suppl/ in the genome. In addition, it was difficult to find L1 RNA doi:10.1073/pnas.2019450117/-/DCSupplemental. outside of the testis and ovary (13). However, in 2005, Muotri www.pnas.org/cgi/doi/10.1073/pnas.2019450117 PNAS Latest Articles | 1of8 Downloaded by guest on September 24, 2021 present in normal cells adjacent to the tumor, similar to previous single-copy sites on different chromosomes. To use the MDA DNA for library findings in gDNA from normal tissues (21, 29). production, we required a positive PCR product from all 16 sites, except for the colon cancer samples, where we worked with cells that had 14 to 16 Materials and Methods positive sites. Even with the highest-quality MDA kit, this stringent criterion was fulfilled in only 0 to 50% of single-cell DNA tested per single FACS- To detect somatic L1 insertions in single cells, we modified previous methods sorting experiment. (36) at both the wet bench and computational phases. These changes led to After MDA and its quality-control procedure, we carried out asymmetric, more efficient detection of somatic L1 insertions and improved accuracy in one-sided PCR off the 3′ ends of human-specific L1s using the specific ACA reducing chimeras. Briefly, we isolated single tumor and nontumor cell nu- sequence 94 bp upstream of the polyA tract (38). To obtain a very high clei by FACS sorting. When possible, we separated aneuploid nuclei on the fraction of 3′ flanking sequences of these L1s, we then circularized the basis of DNA content [nuclei having a DNA content peak greater than a product (Fig. 2) and carried out inverse PCR around the circle in both di- euploid peak: A peak between G1 and G2 (Fig. 1B) or a peak greater than G2 rections using two oligonucleotides, both of which were located on the (Fig. 1D)]. Distance along the abscissa is proportional to DNA content. In L1Hs-specific sequence (SI Appendix, Supplemental Methods). Additional Fig. 1B, aneuploid cells (∼240 to 260) have less DNA than euploid cells (∼260 adapters were then added to the resulting linearized products, increasing to 280), while in Fig. 1D, aneuploid cells (∼260 to 280) have more DNA than the specificity for human-specific L1s by anchoring the 3′ end of the L1 euploid cells (∼180 to 200). primer to the specific G residue in L1Hs 9 bp upstream of the polyA tract. The We then amplified single-cell DNA (∼12 pg) by MDA to 0.5 to 5 μg (37). resulting library was quality-checked for flanking sequences 3′ to human- MDA DNA was then quality-checked by PCR amplification of 16 different specific L1s by topoisomerase cloning and Sanger sequencing of 5 to 10 Fig. 1. FACS analysis of nuclei from cases 352 and 6041. (A) The 352 normal pancreas nuclei; G2 phase (R11) nuclei were sorted. (B) The 352 pancreatic cancer nuclei; G2 phase (R11) and sub G2 (R10) nuclei are sorted. (C) The 6041 normal gastric nuclei; G2 phase (R11) nuclei are sorted.
Load more

Recommended publications
  • Regulation and Dysregulation of Chromosome Structure in Cancer
    Regulation and Dysregulation of Chromosome Structure in Cancer The MIT Faculty has made this article openly available. Please share how this access benefits you. Your story matters. Citation Hnisz, Denes et al. “Regulation and Dysregulation of Chromosome Structure in Cancer.” Annual Review of Cancer Biology 2, 1 (March 2018): 21–40 © 2018 Annual Reviews As Published https://doi.org/10.1146/annurev-cancerbio-030617-050134 Version Author's final manuscript Citable link http://hdl.handle.net/1721.1/117286 Terms of Use Creative Commons Attribution-Noncommercial-Share Alike Detailed Terms http://creativecommons.org/licenses/by-nc-sa/4.0/ Regulation and dysregulation of chromosome structure in cancer Denes Hnisz1*, Jurian Schuijers1, Charles H. Li1,2, Richard A. Young1,2* 1 Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA 2 Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA * Corresponding authors Corresponding Authors: Denes Hnisz Whitehead Institute for Biomedical Research 455 Main Street Cambridge, MA 02142 Tel: (617) 258-7181 Fax: (617) 258-0376 [email protected] Richard A. Young Whitehead Institute for Biomedical Research 455 Main Street Cambridge, MA 02142 Tel: (617) 258-5218 Fax: (617) 258-0376 [email protected] 1 Summary Cancer arises from genetic alterations that produce dysregulated gene expression programs. Normal gene regulation occurs in the context of chromosome loop structures called insulated neighborhoods, and recent studies have shown that these structures are altered and can contribute to oncogene dysregulation in various cancer cells. We review here the types of genetic and epigenetic alterations that influence neighborhood structures and contribute to gene dysregulation in cancer, present models for insulated neighborhoods associated with the most prominent human oncogenes, and discuss how such models may lead to further advances in cancer diagnosis and therapy.
    [Show full text]
  • Universidade Estadual De Campinas Instituto De Biologia
    UNIVERSIDADE ESTADUAL DE CAMPINAS INSTITUTO DE BIOLOGIA VERÔNICA APARECIDA MONTEIRO SAIA CEREDA O PROTEOMA DO CORPO CALOSO DA ESQUIZOFRENIA THE PROTEOME OF THE CORPUS CALLOSUM IN SCHIZOPHRENIA CAMPINAS 2016 1 VERÔNICA APARECIDA MONTEIRO SAIA CEREDA O PROTEOMA DO CORPO CALOSO DA ESQUIZOFRENIA THE PROTEOME OF THE CORPUS CALLOSUM IN SCHIZOPHRENIA Dissertação apresentada ao Instituto de Biologia da Universidade Estadual de Campinas como parte dos requisitos exigidos para a obtenção do Título de Mestra em Biologia Funcional e Molecular na área de concentração de Bioquímica. Dissertation presented to the Institute of Biology of the University of Campinas in partial fulfillment of the requirements for the degree of Master in Functional and Molecular Biology, in the area of Biochemistry. ESTE ARQUIVO DIGITAL CORRESPONDE À VERSÃO FINAL DA DISSERTAÇÃO DEFENDIDA PELA ALUNA VERÔNICA APARECIDA MONTEIRO SAIA CEREDA E ORIENTADA PELO DANIEL MARTINS-DE-SOUZA. Orientador: Daniel Martins-de-Souza CAMPINAS 2016 2 Agência(s) de fomento e nº(s) de processo(s): CNPq, 151787/2F2014-0 Ficha catalográfica Universidade Estadual de Campinas Biblioteca do Instituto de Biologia Mara Janaina de Oliveira - CRB 8/6972 Saia-Cereda, Verônica Aparecida Monteiro, 1988- Sa21p O proteoma do corpo caloso da esquizofrenia / Verônica Aparecida Monteiro Saia Cereda. – Campinas, SP : [s.n.], 2016. Orientador: Daniel Martins de Souza. Dissertação (mestrado) – Universidade Estadual de Campinas, Instituto de Biologia. 1. Esquizofrenia. 2. Espectrometria de massas. 3. Corpo caloso.
    [Show full text]
  • Sequencing-Based Computational Methods for Identifying Impactful Genomic Alterations in Cancers
    Sequencing-based computational methods for identifying impactful genomic alterations in cancers by Isaac Charles Joseph A dissertation submitted in partial satisfaction of the requirements for the degree of Doctor of Philosophy in Computational Biology in the Graduate Division of the University of California, Berkeley Committee in charge: Professor Lior Pachter, Chair Professor Joseph Costello Associate Professor Haiyan Huang Professor Anthony Joseph Fall 2016 Sequencing-based computational methods for identifying impactful genomic alterations in cancers Copyright 2016 by Isaac Charles Joseph 1 Abstract Sequencing-based computational methods for identifying impactful genomic alterations in cancers by Isaac Charles Joseph Doctor of Philosophy in Computational Biology University of California, Berkeley Professor Lior Pachter, Chair Recent advances in collecting sequencing data from tumors is promising for both immediate individual patient treatment and investigation of cancer mechanisms. A resultant central goal is identifying changes in tumors that are impactful towards these ends. Here, we develop two tools to identify impactful changes at different levels. We develop both methods in the context of gliomas, a common form of brain cancer. Firstly, we develop and assess a tool for assessing the impact of fusion genes, a type of common mutation using RNA-sequencing data. We validate the tool by working with collaborators in The Cancer Genome Atlas. Secondly, we develop a tool for an overall assessment of patient outcome by integrating data from diverse sequencing platforms. We validate this tool using simulation, data from consortiums, and collaborators at UCSF. i To those that suffer It is you that have convinced me that there is something still worth fighting for in this world.
    [Show full text]
  • ABSTRACT MITCHELL III, ROBERT DRAKE. Global Human Health
    ABSTRACT MITCHELL III, ROBERT DRAKE. Global Human Health Risks for Arthropod Repellents or Insecticides and Alternative Control Strategies. (Under the direction of Dr. R. Michael Roe). Protein-coding genes and environmental chemicals. New paradigms for human health risk assessment of environmental chemicals emphasize the use of molecular methods and human-derived cell lines. In this study, we examined the effects of the insect repellent DEET (N, N-diethyl-m-toluamide) and the phenylpyrazole insecticide fipronil (fluocyanobenpyrazole) on transcript levels in primary human hepatocytes. These chemicals were tested individually and as a mixture. RNA-Seq showed that 100 µM DEET significantly increased transcript levels for 108 genes and lowered transcript levels for 64 genes and fipronil at 10 µM increased the levels of 2,246 transcripts and decreased the levels for 1,428 transcripts. Fipronil was 21-times more effective than DEET in eliciting changes, even though the treatment concentration was 10-fold lower for fipronil versus DEET. The mixture of DEET and fipronil produced a more than additive effect (levels increased for 3,017 transcripts and decreased for 2,087 transcripts). The transcripts affected in our treatments influenced various biological pathways and processes important to normal cellular functions. Long non-protein coding RNAs and environmental chemicals. While the synthesis and use of new chemical compounds is at an all-time high, the study of their potential impact on human health is quickly falling behind. We chose to examine the effects of two common environmental chemicals, the insect repellent DEET and the insecticide fipronil, on transcript levels of long non-protein coding RNAs (lncRNAs) in primary human hepatocytes.
    [Show full text]
  • Protein Kinase A-Mediated Septin7 Phosphorylation Disrupts Septin Filaments and Ciliogenesis
    cells Article Protein Kinase A-Mediated Septin7 Phosphorylation Disrupts Septin Filaments and Ciliogenesis Han-Yu Wang 1,2, Chun-Hsiang Lin 1, Yi-Ru Shen 1, Ting-Yu Chen 2,3, Chia-Yih Wang 2,3,* and Pao-Lin Kuo 1,2,4,* 1 Department of Obstetrics and Gynecology, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan; [email protected] (H.-Y.W.); [email protected] (C.-H.L.); [email protected] (Y.-R.S.) 2 Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan; [email protected] 3 Department of Cell Biology and Anatomy, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan 4 Department of Obstetrics and Gynecology, National Cheng-Kung University Hospital, Tainan 704, Taiwan * Correspondence: [email protected] (C.-Y.W.); [email protected] (P.-L.K.); Tel.: +886-6-2353535 (ext. 5338); (C.-Y.W.)+886-6-2353535 (ext. 5262) (P.-L.K.) Abstract: Septins are GTP-binding proteins that form heteromeric filaments for proper cell growth and migration. Among the septins, septin7 (SEPT7) is an important component of all septin filaments. Here we show that protein kinase A (PKA) phosphorylates SEPT7 at Thr197, thus disrupting septin filament dynamics and ciliogenesis. The Thr197 residue of SEPT7, a PKA phosphorylating site, was conserved among different species. Treatment with cAMP or overexpression of PKA catalytic subunit (PKACA2) induced SEPT7 phosphorylation, followed by disruption of septin filament formation. Constitutive phosphorylation of SEPT7 at Thr197 reduced SEPT7-SEPT7 interaction, but did not affect SEPT7-SEPT6-SEPT2 or SEPT4 interaction.
    [Show full text]
  • 2021 Western Medical Research Conference
    Abstracts J Investig Med: first published as 10.1136/jim-2021-WRMC on 21 December 2020. Downloaded from Genetics I Purpose of Study Genomic sequencing has identified a growing number of genes associated with developmental brain disorders Concurrent session and revealed the overlapping genetic architecture of autism spectrum disorder (ASD) and intellectual disability (ID). Chil- 8:10 AM dren with ASD are often identified first by psychologists or neurologists and the extent of genetic testing or genetics refer- Friday, January 29, 2021 ral is variable. Applying clinical whole genome sequencing (cWGS) early in the diagnostic process has the potential for timely molecular diagnosis and to circumvent the diagnostic 1 PROSPECTIVE STUDY OF EPILEPSY IN NGLY1 odyssey. Here we report a pilot study of cWGS in a clinical DEFICIENCY cohort of young children with ASD. RJ Levy*, CH Frater, WB Galentine, MR Ruzhnikov. Stanford University School of Medicine, Methods Used Children with ASD and cognitive delays/ID Stanford, CA were referred by neurologists or psychologists at a regional healthcare organization. Medical records were used to classify 10.1136/jim-2021-WRMC.1 probands as 1) ASD/ID or 2) complex ASD (defined as 1 or more major malformations, abnormal head circumference, or Purpose of Study To refine the electroclinical phenotype of dysmorphic features). cWGS was performed using either epilepsy in NGLY1 deficiency via prospective clinical and elec- parent-child trio (n=16) or parent-child-affected sibling (multi- troencephalogram (EEG) findings in an international cohort. plex families; n=3). Variants were classified according to Methods Used We performed prospective phenotyping of 28 ACMG guidelines.
    [Show full text]
  • Adhesion-Dependent Mechanisms Regulating Mitosis
    Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Medicine 1523 Adhesion-dependent mechanisms regulating mitosis DEEPESH KUMAR GUPTA ACTA UNIVERSITATIS UPSALIENSIS ISSN 1651-6206 ISBN 978-91-513-0531-8 UPPSALA urn:nbn:se:uu:diva-368422 2019 Dissertation presented at Uppsala University to be publicly examined in B42 Biomedical Center, Biomedical Center Husargatn 3, Uppsala, Friday, 1 February 2019 at 09:15 for the degree of Doctor of Philosophy (Faculty of Medicine). The examination will be conducted in English. Faculty examiner: Senior Scientist Kaisa Haglund (Oslo University Hospital). Abstract Gupta, D. K. 2019. Adhesion-dependent mechanisms regulating mitosis. Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Medicine 1523. 51 pp. Uppsala: Acta Universitatis Upsaliensis. ISBN 978-91-513-0531-8. Integrin-mediated cell adhesion is required for normal cell cycle progression during G1-S transition and for the completion of cytokinesis. Cancer cells have ability to grow anchorage- independently, but the underlying mechanisms and the functional significance for cancer development are unclear. The current thesis describes new data on the adhesion-linked molecular mechanisms regulating cytokinesis and centrosomes. Non-adherent fibroblast failed in the last step of the cytokinesis process, the abscission. This was due to lack of CEP55-binding of ESCRT-III and its associated proteins to the midbody (MB) in the intercellular bridge (ICB), which in turn correlated with too early disappearance of PLK1 and the consequent premature CEP55 accumulation. Integrin-induced FAK activity was found to be an important upstream step in the regulation of PLK1 and cytokinetic abscission. Under prolonged suspension culture, the MB disappeared but septin filaments kept the ICB in the ingressed state.
    [Show full text]
  • Ongoing Human Chromosome End Extension Revealed by Analysis of Bionano and Nanopore Data Received: 4 May 2018 Haojing Shao , Chenxi Zhou , Minh Duc Cao & Lachlan J
    www.nature.com/scientificreports OPEN Ongoing human chromosome end extension revealed by analysis of BioNano and nanopore data Received: 4 May 2018 Haojing Shao , Chenxi Zhou , Minh Duc Cao & Lachlan J. M. Coin Accepted: 22 October 2018 The majority of human chromosome ends remain incompletely assembled due to their highly repetitive Published: xx xx xxxx structure. In this study, we use BioNano data to anchor and extend chromosome ends from two European trios as well as two unrelated Asian genomes. At least 11 BioNano assembled chromosome ends are structurally divergent from the reference genome, including both missing sequence and extensions. These extensions are heritable and in some cases divergent between Asian and European samples. Six out of nine predicted extension sequences from NA12878 can be confrmed and flled by nanopore data. We identify two multi-kilobase sequence families both enriched more than 100- fold in extension sequence (p-values < 1e-5) whose origins can be traced to interstitial sequence on ancestral primate chromosome 7. Extensive sub-telomeric duplication of these families has occurred in the human lineage subsequent to divergence from chimpanzees. Te genome sequence of chromosome ends in the reference human genome remains incompletely assembled. In the latest draf of the human genome1 21 out of 48 chromosome ends were incomplete; amongst which fve chromosome ends (13p, 14p, 15p, 21p, 22p) are completely unknown and the remaining chromosome ends are capped with 10–110 kb of unknown sequence. Tere are many interesting observations in the chromosome end regions which remain unexplained, such as the observed increase in genetic divergence between Chimpanzee and Humans towards the chromosome ends2.
    [Show full text]
  • Transcriptomics Analysis and Its Applications in Cancer
    Transcriptomics analysis and its applications in cancer Alejandra Cervera Taboada Research Program in Systems Oncology Research Programs Unit Biochemistry and Developmental Biology Medicum Faculty of Medicine University of Helsinki Finland Academic dissertation To be publicly discussed, with the permission of the Faculty of Medicine of the University of Helsinki, on the 14th of December 2020, at 15 o’clock. The defence is open for audience through remote access. Helsinki 2020 Supervisor Sampsa Hautaniemi, DTech, Professor Research Program in Systems Oncology Research Programs Unit Biochemistry and Developmental Biology Medicum Faculty of Medicine University of Helsinki Helsinki, Finland Reviewers appointed by the Faculty Rolf Skotheim, PhD Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital-Radiumhospitalet Oslo, Norway Joaquin Dopazo, PhD, Director Clinical Bioinformatics Area Fundación Progreso y Salud Universidad de Valencia Sevilla, Spain Opponent appointed by the Faculty Carla Daniela Robles Espinoza, PhD International Laboratory for Human Genome Research, National Autonomous University of Mexico Juriquilla, Mexico Faculty of Medicine Doctoral Programme in Biomedicine ISBN 978-951-51-6865-8 (paperback) ISBN 978-951-51-6866-5 (PDF) http://ethesis.helsinki.fi Unigrafia Oy Helsinki 2020 The Faculty of Medicine uses the Urkund system (plagiarism recognition) to exam- ine all doctoral dissertations. "We reveal ourselves in the metaphors we choose for depicting the cosmos in miniature." - Stephen Jay Gould To Antonio, Abstract Cancer is a collection of diseases that combined are one of the leading causes of deaths worldwide. Although great strides have been made in finding cures for certain cancers, the heterogeneity caused by both the tissue in which cancer originates and the mutations acquired in the cell’s DNA results in unsuccessful treatments for some patients.
    [Show full text]
  • Download Cancer Genomics Case Studies
    CANCER RESEARCH Starting at HEME MALIGNANCIES AND $450 SOLID TUMOR RESEARCH per genome Cancer samples are just too complex for low coverage Bionano Genome Imaging uncovers large structural whole genome sequencing. Complex rearrangements variations beyond what short and long read as well as unsequenceable regions of the genome sequencing can see. present an additional challenge for short and long read Bionano Genome Imaging directly visualizes patterns of sequencing technologies. labels on megabase-size intact DNA molecules, at up to 1600X coverage, to detect structural variations. Every type Bionano Genome Imaging detects unbiased of structural variant is detected with sensitivities as high as structural variations at sensitives much higher than 99%, and with positive predictive value of more than 97%. sequencing based technologies, and down to It can detect balanced translocations, repeat expansions, 1% variant allele fraction. events flanked by repeats, and even rearrangements of large segmental duplications. Unlike sequencing based methods, that Extreme genomic rearrangements are hallmarks of cancer are typically unable to detect insertions or identify where the manifestation. Deciphering such complex genomic structures extra sequence is inserted, Bionano detects both deletions and requires a combination of short read sequencing as well as long insertions starting at 500 bp with high sensitivity. And because range information with high coverage to unlock the heterogeneity it uses a single molecule imaging technology, mosaic variants while providing a complete picture of the genome. To date, NGS down to as little as 1% variant allele fraction can be detected applications in the clinic are limited to either low coverage across as well. the whole genome, or high coverage exome sequencing that disregards 98% of the genome.
    [Show full text]
  • Clinical Research 2021 Sections
    Sackler Faculty of Medicine Clinical Research 2021 Sections Cancer 6 Cardiovascular System 41 Digestive System 57 Endocrine Disease 82 Genetic Diseases & Genomics 100 Immunology & Hematology 121 Infectious Diseases 133 Musculoskeletal Disorders 140 Neurological & Psychiatric Diseases 151 Ophthalmology 187 Public Health 197 Reproduction 205 Stem Cells & Regenerative Medicine 209 Renal System 220 Cover images (from bottom left, clockwise): Image 1: Staining of a novel anti-frizzled7 monoclonal antibody directed at tumor stem Cells. Credit: Benjamin Dekel lab. Image 2: Growing adult kidney spheroids and organoids for cell therapy. Credit: Benjamin Dekel lab. Image 3 & 4: Vibrio proteolyticus bacteria infecting macrophages. Credit: Dor Salomon. Image 5: K562 leukemia cells responding to complement attack (red-complement C9, green-mitochondrial stress protein mortalin) Credit: Niv Mazkereth, Zvi Fishelson. Image 6: Cardiomyocyte proliferation in newborn mouse heart by phosphohistone 3 staining (purple). Credit: Jonathan Leor. © All rights reserved Editor: Prof. Karen Avraham Graphic design: Michal Semo Kovetz, TAU Graphic Design Studio June 2021 Sackler Faculty of Medicine Research 2021 2 The Sackler Faculty of Medicine The Sackler Faculty of Medicine is Israel’s largest diabetes, neurodegenerative diseases, infectious medical research and training complex. The Sackler diseases and genetic diseases, including but not Faculty of Medicine of Tel Aviv University (TAU) was imited to Alzheimer’s disease, Parkinson’s disease founded in 1964 following the generous contributions and HIV/AIDS. Physicians in 181 Sacker affiliated of renowned U.S. doctors and philanthropists departments and institutes in 17 hospitals hold Raymond, and the late Mortimer and Arthur Sackler. academic appointments at TAU. The Gitter-Smolarz Research at the Sackler Faculty of Medicine is Life Sciences and Medicine Library serves students multidisciplinary, as scientists and clinicians combine and staff and is the center of a consortium of 15 efforts in basic and translational research.
    [Show full text]
  • EGFR in Cancer: Signaling Mechanisms, Drugs, and Acquired Resistance
    cancers Review EGFR in Cancer: Signaling Mechanisms, Drugs, and Acquired Resistance Mary Luz Uribe , Ilaria Marrocco and Yosef Yarden * Department of Biological Regulation, Weizmann Institute of Science, Rehovot 7610001, Israel; [email protected] (M.L.U.); [email protected] (I.M.) * Correspondence: [email protected] Simple Summary: Growth factors are hormone-like molecules able to promote division and mi- gration of normal cells, but cancer captured the underlying mechanisms to unleash tumor growth and metastasis. Here we review the epidermal growth factor (EGF), which controls epithelial cells, the precursors of all carcinomas, and the cognate cell surface receptor, called EGFR. In addition to over-production of EGF and its family members in tumors, EGFR is similarly over-produced, and mutant hyper-active forms of EGFR are uniquely found in some brain, lung, and other cancers. After describing the biochemical mechanisms underlying the cancer-promoting actions of EGFR, we review some of the latest research discoveries and list all anti-cancer drugs specifically designed to block the EGFR’s biochemical pathway. We conclude by explaining why some patients with lung or colorectal cancer do not respond to the anti-EGFR therapies and why still other patients, who initially respond, become tolerant to the drugs. Abstract: The epidermal growth factor receptor (EGFR) has served as the founding member of the large family of growth factor receptors harboring intrinsic tyrosine kinase function. High abundance of EGFR and large internal deletions are frequently observed in brain tumors, whereas Citation: Uribe, M.L.; Marrocco, I.; point mutations and small insertions within the kinase domain are common in lung cancer.
    [Show full text]