NGI is still up and running during the Covid-19 pandemic, but we are experiencing some limitations in terms of personnel and key reagents. Each NGI node is following its respective host university recommendations and will continue operation until further notice.
The Illumina NovaSeq 6000 system is the largest of the Illumina sequencing instruments, able to run two flow cells independently of each other and generate massive sequencing depth at competitive prices.
Long-read sequencing can resolve regions of the genome that are inaccessible to short reads, and therefore are ideal for genome-gap closure, solving structural rearrangements and sequencing through repetitive elements. Here we introduce the Xdrop technology: a novel microfluidic-based system that allows for targeted enrichment of long DNA molecules starting from only a few nanograms of DNA. Xdrop is based on isolation of long DNA fragments in millions of droplets, where the droplets containing a target sequence of interest are fluorescently labeled and sorted using flow cytometry. The final product from the Xdrop procedure is an enriched population of long DNA molecules that can be investigated by sequencing. To demonstrate the capability of Xdrop, we performed enrichment of the human papilloma virus (HPV) 18 integrated in the genome of human HeLa cells. Analysis of the sequencing reads resolved three HPV18-chr8 integrations at base pair resolution, and the captured fragments extended up to 30 kb into the human genome at the integration sites. Further, we enriched the complete TP53 locus in a leukemia cell line and could successfully phase co-existing mutations using PacBio sequencing. In summary, our results show that Xdrop is an efficient enrichment technology for studying complex genomic regions. This article is protected by copyright. All rights reserved.
Combining ERBB family and MET inhibitors is an effective therapeutic strategy in cutaneous malignant melanoma independent of BRAF/NRAS mutation status.
I Das, M Wilhelm, V Höiom, R Franco Marquez, F Costa Svedman, J Hansson, R Tuominen, S Egyhàzi Brage
Cell Death Dis, 10 (9) 2041-4889 (2019)
Current treatment modalities for disseminated cutaneous malignant melanoma (CMM) improve survival; however, relapses are common. A number of receptor tyrosine kinases (RTKs) including EGFR and MET have been reported to be involved in CMM metastasis and in the development of resistance to therapy, targeting the mitogen-activated protein kinase (MAPK pathway). IHC analysis showed that patients with higher MET protein expression had a significantly shorter overall survival. In addition, silencing of MET caused an upregulation of EGFR and p-AKT, which was abrogated by concomitant silencing of MET and EGFR in CMM cells resistant to MAPK-targeting drugs. We therefore explored novel treatment strategies using clinically approved drugs afatinib (ERBB family inhibitor) and crizotinib (MET inhibitor), to simultaneously block MET and ERBB family RTKs. The effects of the combination were assessed in cell culture and spheroid models using established CMM and patient-derived short-term cell lines, and an in vivo xenograft mouse model. The combination had a synergistic effect, promoting cell death, concomitant with a potent downregulation of migratory and invasive capacity independent of their BRAF/NRAS mutational status. Furthermore, the combination attenuated tumor growth rate, as ascertained by the significant reduction of Ki67 expression and induced DNA damage in vivo. Importantly, this combination therapy had minimal therapy-related toxicity in mice. Lastly, the cell cycle G2 checkpoint kinase WEE1 and the RTK IGF1R, non-canonical targets, were altered upon exposure to the combination. Knockdown of WEE1 abrogated the combination-mediated effects on cell migration and proliferation in BRAF mutant BRAF inhibitor-sensitive cells, whereas WEE1 silencing alone inhibited cell migration in NRAS mutant cells. In summary, our results show that afatinib and crizotinib in combination is a promising alternative targeted therapy option for CMM patients, irrespective of BRAF/NRAS mutational status, as well as for cases where resistance has developed towards BRAF inhibitors.
Novel Viruses Found in Antricola Ticks Collected in Bat Caves in the Western Amazonia of Brazil.
AL Blomström, HR Luz, P Öhlund, M Lukenge, PE Brandão, MB Labruna, M Berg
Viruses, 12 (1) 1999-4915 (2019)
In this study, we describe the viral composition of adult Antricoladelacruzi ticks collected in a hot bat cave in the state of Rondônia, Western Amazonia, Brazil. A.delacruzi ticks, are special, compared to many other ticks, in that they feed on both bats (larval blood feeding) and bat guano (nymphal and adult feeding) instead of feeding exclusively on vertebrate hosts (blood feeding). Considering this unique life-cycle it is potentially possible that these ticks can pick up/be infected by viruses not only present in the blood of viremic bats but also by virus shed through the bat guano. The viral metagenomic investigation of adult ticks showed that single-stranded negative-sense RNA viruses were the dominant group of viruses identified in the investigated ticks. Out of these, members of the Nairoviridae family were in clear majority constituting 88% of all viral reads in the data set. Genetic and phylogenetic analyses indicate the presence of several different orthonairoviruses in the investigated ticks with only distant relationship to previously described ones. In addition, identification of viral sequences belonging to Orthomyxoviridae, Iflaviridae, Dicistroviridae, Polycipiviridae, Reoviridae and different unclassified RNA viruses showed the presence of viruses with low sequence similarity to previously described viruses.
Oral Microbiota Profile Associates with Sugar Intake and Taste Preference Genes.
A Esberg, S Haworth, P Hasslöf, P Lif Holgerson, I Johansson
Nutrients, 12 (3) 2072-6643 (2020)
Oral microbiota ecology is influenced by environmental and host conditions, but few studies have evaluated associations between untargeted measures of the entire oral microbiome and potentially relevant environmental and host factors. This study aimed to identify salivary microbiota cluster groups using hierarchical cluster analyses (Wards method) based on 16S rRNA gene amplicon sequencing, and identify lifestyle and host factors which were associated with these groups. Group members ( n = 175) were distinctly separated by microbiota profiles and differed in reported sucrose intake and allelic variation in the taste-preference-associated genes TAS1R1 (rs731024) and GNAT3 (rs2074673). Groups with higher sucrose intake were either characterized by a wide panel of species or phylotypes with fewer aciduric species, or by a narrower profile that included documented aciduric- and caries-associated species. The inferred functional profiles of the latter type were dominated by metabolic pathways associated with the carbohydrate metabolism with enrichment of glycosidase functions. In conclusion, this study supported in vivo associations between sugar intake and oral microbiota ecology, but it also found evidence for a variable microbiota response to sugar, highlighting the importance of modifying host factors and microbes beyond the commonly targeted acidogenic and acid-tolerant species. The results should be confirmed under controlled settings with comprehensive phenotypic and genotypic data.
Preclinical safety studies of human embryonic stem cell-derived retinal pigment epithelial cells for the treatment of age-related macular degeneration.
S Petrus-Reurer, P Kumar, S Padrell Sánchez, M Aronsson, H André, H Bartuma, A Plaza Reyes, EF Nandrot, A Kvanta, F Lanner
Stem Cells Transl Med, 2157-6580 (2020)
As pluripotent stem cell (PSC)-based reparative cell therapies are reaching the bedside, there is a growing need for the standardization of studies concerning safety of the derived products. Clinical trials using these promising strategies are in development, and treatment for age-related macular degeneration is one of the first that has reached patients. We have previously established a xeno-free and defined differentiation protocol to generate functional human embryonic stem cells (hESCs)-derived retinal pigment epithelial (RPE) cells. In this study, we perform preclinical safety studies including karyotype and whole-genome sequencing to assess genome stability, single cell RNA sequencing to ensure cell purity, and biodistribution and tumorigenicity analysis to rule out potential migratory or tumorigenic properties of these cells. Whole-genome sequencing analysis illustrates that existing germline variants load is higher than the introduced variants acquired through in vitro culture or differentiation, and enforces the importance to examine the genome integrity at a deeper level than just karyotype. Altogether, we provide a strategy for preclinical evaluation of PSC-based therapies and the data support safety of the hESC-RPE cells generated through our in vitro differentiation methodology.
Multi-ancestry GWAS of the electrocardiographic PR interval identifies 202 loci underlying cardiac conduction
I Ntalla, LC Weng, JH Cartwright, AW Hall, G Sveinbjornsson, NR Tucker, SH Choi, MD Chaffin, C Roselli, MR Barnes, B Mifsud, HR Warren, C Hayward, J Marten, JJ Cranley, MP Concas, P Gasparini, T Boutin, I Kolcic, O Polasek, I Rudan, NM Araujo, MF Lima-Costa, ALP Ribeiro, RP Souza, E Tarazona-Santos, V Giedraitis, E Ingelsson, A Mahajan, AP Morris, F Del Greco M, L Foco, M Gögele, AA Hicks, JP Cook, L Lind, CM Lindgren, J Sundström, CP Nelson, MB Riaz, NJ Samani, G Sinagra, S Ulivi, M Kähönen, PP Mishra, N Mononen, K Nikus, MJ Caulfield, A Dominiczak, S Padmanabhan, ME Montasser, JR O’Connell, K Ryan, AR Shuldiner, S Aeschbacher, D Conen, L Risch, S Thériault, N Hutri-Kähönen, T Lehtimäki, LP Lyytikäinen, OT Raitakari, CLK Barnes, H Campbell, PK Joshi, JF Wilson, A Isaacs, JA Kors, CM van Duijn, PL Huang, V Gudnason, TB Harris, LJ Launer, AV Smith, EP Bottinger, RJF Loos, GN Nadkarni, MH Preuss, A Correa, H Mei, J Wilson, T Meitinger, M Müller-Nurasyid, A Peters, M Waldenberger, M Mangino, TD Spector, M Rienstra, YJ van de Vegte, P van der Harst, N Verweij, S Kääb, K Schramm, MF Sinner, K Strauch, MJ Cutler, D Fatkin, B London, M Olesen, DM Roden, M Benjamin Shoemaker, J Gustav Smith, ML Biggs, JC Bis, JA Brody, BM Psaty, K Rice, N Sotoodehnia, A De Grandi, C Fuchsberger, C Pattaro, PP Pramstaller, I Ford, J Wouter Jukema, PW Macfarlane, S Trompet, M Dörr, SB Felix, U Völker, S Weiss, AS Havulinna, A Jula, K Sääksjärvi, V Salomaa, X Guo, SR Heckbert, HJ Lin, JI Rotter, KD Taylor, J Yao, R de Mutsert, AC Maan, DO Mook-Kanamori, R Noordam, F Cucca, J Ding, EG Lakatta, Y Qian, KV Tarasov, D Levy, H Lin, CH Newton-Cheh, KL Lunetta, AD Murray, DJ Porteous, BH Smith, BH Stricker, A Uitterlinden, ME van den Berg, J Haessler, RD Jackson, C Kooperberg, U Peters, AP Reiner, EA Whitsel, A Alonso, DE Arking, E Boerwinkle, GB Ehret, EZ Soliman, CL Avery, SM Gogarten, KF Kerr, CC Laurie, AA Seyerle, A Stilp, S Assa, M Abdullah Said, M Yldau van der Ende, PD Lambiase, M Orini, J Ramirez, S Van Duijvenboden, DO Arnar, DF Gudbjartsson, H Holm, P Sulem, G Thorleifsson, RB Thorolfsdottir, U Thorsteinsdottir, EJ Benjamin, A Tinker, K Stefansson, PT Ellinor, Y Jamshidi, SA Lubitz, PB Munroe
Molecular characterization of a large unselected cohort of metastatic colorectal cancers in relation to primary tumor location, rare metastatic sites and prognosis.
L Nunes, K Aasebø, L Mathot, V Ljungström, PH Edqvist, M Sundström, A Dragomir, P Pfeiffer, A Ameur, F Ponten, A Mezheyeuski, H Sorbye, T Sjöblom, B Glimelius
NGI CollaborationActa Oncol, 1651-226X (2020)
Background: We have reported that BRAF V600E mutations and microsatellite instability-high (MSI-H) are more prevalent in a population-based cohort of metastatic colorectal cancer (mCRC) patients than has been reported from clinical trials or hospital-based patient groups. The aim was to explore if other mutations in mCRC differ in prevalence between these cohorts in relation to mismatch repair status and primary tumor location and if presence of bone or brain metastases is associated with any mutations.Material and methods: A population-based cohort of 798 mCRC patients from three regions in Scandinavia was used. Forty-four cancer related genes were investigated in a custom designed Ampliseq hotspot panel. Differences in survival were analyzed using the Kaplan-Meier estimator and the Cox regression analysis.Results: Determination of mutations was possible in 449/501 patients for 40/44 genes. Besides BRAF V600E, seen in 19% of the tumors, none of the other mutations appeared more prevalent than in trial cohorts. BRAF V600E and MSI-H, seen in 8%, were associated with poor prognosis as was right-sided primary tumor location (39%) when compared to left-sided and rectum together; however, in a multivariable regression, only the BRAF mutation retained its statistical significance. No other mutations were associated with poor prognosis. ERBB2 alterations were more common if bone metastases were present at diagnosis (17% vs. 4%, p = .011). No association was found for brain metastases. Fifty-two percent had an alteration that is treatable with an FDA-approved targeted therapy, chiefly by EGFR-inhibitor for RAS wild-type and a check-point inhibitor for MSI-H tumors.Conclusions: Right-sided tumor location, BRAF V600E mutations, but no other investigated mutation, and MSI-H are more commonly seen in an unselected cohort than is reported from clinical patient cohorts, likely because they indicate poor prognosis. Half of the patients have a tumor that is treatable with an already FDA-approved targeted drug for mCRC.