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PubMed Publications| Keyword search (4,163 papers available) |  |
"genomics" Keyword-tagged Publications:
| Title | Authors | PubMed ID | |
|---|---|---|---|
| 1 | Integrated metabolomics and metagenomics analysis identifies a unique signature characterizing metabolic syndrome | Wannaiampikul S; Lee B; Chen J; Prentice KJ; Ayansola R; Xu A; Santosa S; Pantopoulos K; Sweeney G; | 41794383 HKAP |
| 2 | Season and city shape urban bioaerosol composition beyond vegetation and socioeconomic gradients | Poirier S; Rondeau-Leclaire J; Faticov M; Roy A; Lajeunesse G; Lucier JF; Tardif S; Kembel SW; Ziter C; Laprise C; Paquette A; Girard C; Laforest-Lapointe I; | 41785576 BIOLOGY |
| 3 | Cross-species evaluation of TANGO2 homologs, including HRG-9 and HRG-10 in em Caenorhabditis elegans, /em challenges a proposed role in heme trafficking | Sandkuhler SE; Youngs KS; Gottipalli O; Owlett LD; Bandora MB; Naaz A; Kim E; Wang L; Wojtovich A; Gupta V; Sacher M; Mackenzie SJ; | 41504601 BIOLOGY |
| 4 | Geography, Ancestry, Age and Sex Shape Somatic Autosomal Mosaic Chromosomal Alterations in Blood | Won Kang JR; Kim YJ; Skead K; Soave D; Evans J; Bruat V; Harwood MP; Morris Q; Matovu E; Mulindwa J; Noyes H; McLeod A; Hazelhurst S; Lombard Z; Ramsay M; Fave MJ; Awadalla P; | 41282824 BIOLOGY |
| 5 | Imaging flow cytometry-based cellular screening elucidates pathophysiology in individuals with Variants of Uncertain Significance | Muffels IJJ; Waterham HR; D' Alessandro G; Zagnoli-Vieira G; Sacher M; Lefeber DJ; Van der Vinne C; Roifman CM; Gassen KLI; Rehmann H; Van Haaften-Visser DY; Nieuwenhuis ESS; Jackson SP; Fuchs SA; Wijk F; van Hasselt P; | 39920830 BIOLOGY |
| 6 | Widespread admixture blurs population structure and confounds Lake Trout (Salvelinus namaycush) conservation even in the genomic era | Bernos TA; Gibelli J; Michaelides S; Won H; Jeon HB; Marin K; Boguski DA; Janjua MY; Gallagher CP; Howland KL; Fraser DJ; | 39730611 BIOLOGY |
| 7 | Evolution of chromosome-arm aberrations in breast cancer through genetic network rewiring | Kuzmin E; Baker TM; Lesluyes T; Monlong J; Abe KT; Coelho PP; Schwartz M; Del Corpo J; Zou D; Morin G; Pacis A; Yang Y; Martinez C; Barber J; Kuasne H; Li R; Bourgey M; Fortier AM; Davison PG; Omeroglu A; Guiot MC; Morris Q; Kleinman CL; Huang S; Gingras AC; Ragoussis J; Bourque G; Van Loo P; Park M; | 38517886 BIOLOGY |
| 8 | Editorial: Computational systems immunovirology | Zarei Ghobadi M; Teymoori-Rad M; Selvaraj G; Wei DQ; | 37475870 CHEMBIOCHEM |
| 9 | Rethinking microbial infallibility in the metagenomics era | O' Malley MA; Walsh DA; | 34160589 BIOLOGY |
| 10 | ChIP-seq protocol for sperm cells and embryos to assess environmental impacts and epigenetic inheritance | Lismer A; Lambrot R; Lafleur C; Dumeaux V; Kimmins S; | 34159325 PERFORM |
| 11 | A Novel Freshwater to Marine Evolutionary Transition Revealed within Methylophilaceae Bacteria from the Arctic Ocean | Ramachandran A; McLatchie S; Walsh DA; | 34154421 BIOLOGY |
| 12 | Identification of a Novel Biosynthetic Gene Cluster in Aspergillus niger Using Comparative Genomics | Evdokias G; Semper C; Mora-Ochomogo M; Di Falco M; Nguyen TTM; Savchenko A; Tsang A; Benoit-Gelber I; | 34064722 BIOLOGY |
| 13 | Core Competencies in Cancer Genomics for Healthcare Professionals: Results From a Systematic Literature Review and a Delphi Process. | Hoxhaj I, Tognetto A, Acampora A, Stojanovic J, Boccia S | 33442861 HKAP |
| 14 | Phylogenomic fingerprinting of tempo and functions of horizontal gene transfer within ochrophytes. | Dorrell RG, Villain A, Perez-Lamarque B, Audren de Kerdrel G, McCallum G, Watson AK, Ait-Mohamed O, Alberti A, Corre E, Frischkorn KR, Pierella Karlusich JJ, Pelletier E, Morlon H, Bowler C, Blanc G | 33419955 BIOLOGY |
| 15 | Genome Sequence Resource of Bacillus velezensis EB14, a native endophytic bacterial strain with biocontrol potential against the poplar stem canker causative pathogen, Sphaerulina musiva. | Naik S, Tsang A, Ramanan US, Dayanandan S | 33263425 BIOLOGY |
| 16 | Functional analysis of low-grade glioma genetic variants predicts key target genes and transcription factors. | Manjunath M; Yan J; Youn Y; Drucker KL; Kollmeyer TM; McKinney AM; Zazubovich V; Zhang Y; Costello JF; Eckel-Passow J; Selvin PR; Jenkins RB; Song JS; | 33130899 PHYSICS |
| 17 | Sediment Metagenomes as Time Capsules of Lake Microbiomes. | Garner RE; Gregory-Eaves I; Walsh DA; | 33148818 BIOLOGY |
| 18 | Size reductions and genomic changes within two generations in wild walleye populations: associated with harvest? | Bowles E, Marin K, Mogensen S, MacLeod P, Fraser DJ | 32684951 CONCORDIA |
| 19 | Plasma levels of one-carbon metabolism nutrients in women with anorexia nervosa | Burdo J; Booij L; Kahan E; Thaler L; Israël M; Agellon LB; Nitschmann E; Wykes L; Steiger H; | 32427359 PSYCHOLOGY |
| 20 | Diversity, evolution, and classification of virophages uncovered through global metagenomics. | Paez-Espino D, Zhou J, Roux S, Nayfach S, Pavlopoulos GA, Schulz F, McMahon KD, Walsh D, Woyke T, Ivanova NN, Eloe-Fadrosh EA, Tringe SG, Kyrpides NC | 31823797 BIOLOGY |
| 21 | Enzymes of early-diverging, zoosporic fungi. | Lange L, Barrett K, Pilgaard B, Gleason F, Tsang A | 31309267 CSFG |
| 22 | Chaco Canyon Dig Unearths Ethical Concerns. | Claw KG, Lippert D, Bardill J, Cordova A, Fox K, Yracheta JM, Bader AC, Bolnick DA, Malhi RS, TallBear K, Garrison NA | 29745246 CONCORDIA |
| 23 | Genetics of mating in members of the Chaetomiaceae as revealed by experimental and genomic characterization of reproduction in Myceliophthora heterothallica. | Hutchinson MI, Powell AJ, Tsang A, O'Toole N, Berka RM, Barry K, Grigoriev IV, Natvig DO | 26608618 CSFG |
| 24 | An Evolutionarily Conserved Transcriptional Activator-Repressor Module Controls Expression of Genes for D-Galacturonic Acid Utilization in Aspergillus niger. | Niu J, Alazi E, Reid ID, Arentshorst M, Punt PJ, Visser J, Tsang A, Ram AF | 28049705 CSFG |
| 25 | Thermostable xylanases from thermophilic fungi and bacteria: Current perspective. | Chadha BS, Kaur B, Basotra N, Tsang A, Pandey A | 30679061 CSFG |
| Title: | Evolution of chromosome-arm aberrations in breast cancer through genetic network rewiring | ||||
| Authors: | Kuzmin E, Baker TM, Lesluyes T, Monlong J, Abe KT, Coelho PP, Schwartz M, Del Corpo J, Zou D, Morin G, Pacis A, Yang Y, Martinez C, Barber J, Kuasne H, Li R, Bourgey M, Fortier AM, Davison PG, Omeroglu A, Guiot MC, Morris Q, Kleinman CL, Huang S, Gingras AC, Ragoussis J, Bourque G, Van Loo P, Park M | ||||
| Link: | https://pubmed.ncbi.nlm.nih.gov/38517886/ | ||||
| DOI: | 10.1016/j.celrep.2024.113988 | ||||
| Publication: | Cell reports | ||||
| Keywords: | CP: Cancer; CP: Genomics; GCK-III; PDCD10; aneuploidy; basal breast cancer; cancer evolution; chromosomal arm copy number aberrations; chromosome 4p; triple-negative breast cancer; | ||||
| PMID: | 38517886 | Category: | Date Added: | 2024-03-22 | |
| Dept Affiliation: |
BIOLOGY
1 Rosalind and Morris Goodman Cancer Institute, Montreal, QC H3A 1A3, Canada; Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada. Electronic address: elena.kuzmin@mcgill.ca. 2 The Francis Crick Institute, NW1 1AT London, UK. 3 Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada; McGill Genome Centre, Montreal, QC H3A 0G1, Canada. 4 Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health, Toronto, ON M5G 1X5, Canada. 5 Rosalind and Morris Goodman Cancer Institute, Montreal, QC H3A 1A3, Canada; Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada. 6 Department of Biology, Concordia University, Montreal, QC H4B 1R6, Canada. 7 Rosalind and Morris Goodman Cancer Institute, Montreal, QC H3A 1A3, Canada. 8 McGill Genome Centre, Montreal, QC H3A 0G1, Canada; Canadian Centre for Computational Genomics (C3G), McGill University, Montreal, QC H3A 0G1, Canada. 9 Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada. 10 Rosalind and Morris Goodman Cancer Institute, Montreal, QC H3A 1A3, Canada; Department of Pathology, McGill University, Montreal, QC H3A 2B4, Canada; Gerald Bronfman Department of Oncology, McGill University, Montreal, QC H4A 3T2, Canada. 11 Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Vector Institute, Toronto, ON M5G 1M1, Canada; Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada; Computational and Systems Biology, Sloan Kettering Institute, New York City, NY 10065, USA. 12 Department of Surgery, McGill University, Montreal, QC H3G 1A4, Canada; McGill University Health Centre, Montreal, QC H4A 3J1, Canada. 13 Department of Pathology, McGill University, Montreal, QC H3A 2B4, Canada. 14 Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Vector Institute, Toronto, ON M5G 1M1, Canada; Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada; Computational and Systems Biology, Sloan Kettering Institute, New York City, NY 10065, USA; Gerstner Sloan Kettering Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA. 15 Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada; Lady Davis Institute for Medical Research, Montreal, QC H3T 1E2, Canada. 16 Rosalind and Morris Goodman Cancer Institute, Montreal, QC H3A 1A3, Canada; Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada; Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada. 17 Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada; McGill Genome Centre, Montreal, QC H3A 0G1, Canada; Canadian Centre for Computational Genomics (C3G), McGill University, Montreal, QC H3A 0G1, Canada. 18 The Francis Crick Institute, NW1 1AT London, UK; Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA. 19 Rosalind and Morris Goodman Cancer Institute, Montreal, QC H3A 1A3, Canada; Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada; Gerald Bronfman Department of Oncology, McGill University, Montreal, QC H4A 3T2, Canada. Electronic address: morag.park@mcgill.ca. |
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Description: |
The basal breast cancer subtype is enriched for triple-negative breast cancer (TNBC) and displays consistent large chromosomal deletions. Here, we characterize evolution and maintenance of chromosome 4p (chr4p) loss in basal breast cancer. Analysis of The Cancer Genome Atlas data shows recurrent deletion of chr4p in basal breast cancer. Phylogenetic analysis of a panel of 23 primary tumor/patient-derived xenograft basal breast cancers reveals early evolution of chr4p deletion. Mechanistically we show that chr4p loss is associated with enhanced proliferation. Gene function studies identify an unknown gene, C4orf19, within chr4p, which suppresses proliferation when overexpressed-a member of the PDCD10-GCKIII kinase module we name PGCKA1. Genome-wide pooled overexpression screens using a barcoded library of human open reading frames identify chromosomal regions, including chr4p, that suppress proliferation when overexpressed in a context-dependent manner, implicating network interactions. Together, these results shed light on the early emergence of complex aneuploid karyotypes involving chr4p and adaptive landscapes shaping breast cancer genomes. |
