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Hasan MDN, Rahman MDM, Husna AA, Kato D, Nakagawa T, Arif M, Miura N. Hypoxia-related Y RNA fragments as a novel potential biomarker for distinguishing metastatic oral melanoma from non-metastatic oral melanoma in dogs. Vet Q 2024; 44:1-8. [PMID: 38288969 PMCID: PMC10829814 DOI: 10.1080/01652176.2023.2300943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 12/27/2023] [Indexed: 02/01/2024] Open
Abstract
Hypoxia may promote tumor progression, and hypoxically altered noncoding RNA (ncRNA) expression may play a role in metastasis. Canine oral melanoma (COM) frequently metastasizes, and ncRNA expression under hypoxia may be clinically significant. We aimed to elucidate ncRNA fragments whose expression is altered by hypoxia in COM-derived primary KMeC and metastatic LMeC cell lines using next-generation sequencing to validate these results in qRT-PCR, and then compare expression between metastatic and non-metastatic COM. The NGS analysis and subsequent qRT-PCR validation were performed using hypoxic and normoxic KMeC and LMeC cells, and clinical samples [tumor tissue, plasma, and plasma-derived extracellular vesicles] obtained from dogs with metastatic or non-metastatic melanoma were analyzed with qRT-PCR. Y RNA was significantly decreased in metastatic LMeC cells versus primary KMeC cells in hypoxic and normoxic conditions. The expression of Y RNA was decreased in dogs with metastatic melanoma versus those with non-metastatic melanoma for all clinical sample types, reflecting the pattern found with hypoxia. Receiver operating characteristic analysis demonstrated that Y RNA level is a promising biomarker for discriminating metastatic from non-metastatic melanoma in plasma [area under the curve (AUC) = 0.993, p < 0.0001] and plasma-derived extracellular vesicles (AUC = 0.981, p = 0.0002). Overall, Y RNA may be more resistant to hypoxic stress in the metastatic than the non-metastatic state for COM. However, further investigation is required to elucidate the biological functions of Y RNA under hypoxic conditions.
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Affiliation(s)
- MD Nazmul Hasan
- Joint Graduate School of Veterinary Medicine, Kagoshima University, Korimoto, Kagoshima, Japan
- Veterinary Teaching Hospital, Joint Faculty of Veterinary Medicine, Kagoshima University, Korimoto, Kagoshima, Kagoshima, Japan
| | - MD Mahfuzur Rahman
- Department of Human Oncology, University of WI School of Medicine and Public Health, Madison, WI, USA
| | - Al Asmaul Husna
- Veterinary Teaching Hospital, Joint Faculty of Veterinary Medicine, Kagoshima University, Korimoto, Kagoshima, Kagoshima, Japan
| | - Daiki Kato
- Laboratory of Veterinary Surgery, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Takayuki Nakagawa
- Laboratory of Veterinary Surgery, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Mohammad Arif
- Joint Graduate School of Veterinary Medicine, Kagoshima University, Korimoto, Kagoshima, Japan
| | - Naoki Miura
- Joint Graduate School of Veterinary Medicine, Kagoshima University, Korimoto, Kagoshima, Japan
- Veterinary Teaching Hospital, Joint Faculty of Veterinary Medicine, Kagoshima University, Korimoto, Kagoshima, Kagoshima, Japan
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Collinson RJ, Wilson L, Boey D, Ng ZY, Mirzai B, Chuah HS, Howman R, Grove CS, Malherbe JAJ, Leahy MF, Linden MD, Fuller KA, Erber WN, Guo BB. Transcription factor 3 is dysregulated in megakaryocytes in myelofibrosis. Platelets 2024; 35:2304173. [PMID: 38303515 DOI: 10.1080/09537104.2024.2304173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 01/02/2024] [Indexed: 02/03/2024]
Abstract
Transcription factor 3 (TCF3) is a DNA transcription factor that modulates megakaryocyte development. Although abnormal TCF3 expression has been identified in a range of hematological malignancies, to date, it has not been investigated in myelofibrosis (MF). MF is a Philadelphia-negative myeloproliferative neoplasm (MPN) that can arise de novo or progress from essential thrombocythemia [ET] and polycythemia vera [PV] and where dysfunctional megakaryocytes have a role in driving the fibrotic progression. We aimed to examine whether TCF3 is dysregulated in megakaryocytes in MPN, and specifically in MF. We first assessed TCF3 protein expression in megakaryocytes using an immunohistochemical approach analyses and showed that TCF3 was reduced in MF compared with ET and PV. Further, the TCF3-negative megakaryocytes were primarily located near trabecular bone and had the typical "MF-like" morphology as described by the WHO. Genomic analysis of isolated megakaryocytes showed three mutations, all predicted to result in a loss of function, in patients with MF; none were seen in megakaryocytes isolated from ET or PV marrow samples. We then progressed to transcriptomic sequencing of platelets which showed loss of TCF3 in MF. These proteomic, genomic and transcriptomic analyses appear to indicate that TCF3 is downregulated in megakaryocytes in MF. This infers aberrations in megakaryopoiesis occur in this progressive phase of MPN. Further exploration of this pathway could provide insights into TCF3 and the evolution of fibrosis and potentially lead to new preventative therapeutic targets.
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Affiliation(s)
- Ryan J Collinson
- School of Biomedical Sciences, The University of Western Australia, Crawley, WA, Australia
| | - Lynne Wilson
- School of Biomedical Sciences, The University of Western Australia, Crawley, WA, Australia
| | - Darren Boey
- School of Biomedical Sciences, The University of Western Australia, Crawley, WA, Australia
| | - Zi Yun Ng
- School of Biomedical Sciences, The University of Western Australia, Crawley, WA, Australia
- Department of Haematology, Royal Perth Hospital, Perth, WA, Australia
| | - Bob Mirzai
- PathWest Laboratory Medicine, Nedlands, WA, Australia
| | - Hun S Chuah
- Department of Haematology, Royal Perth Hospital, Perth, WA, Australia
- PathWest Laboratory Medicine, Nedlands, WA, Australia
- Department of Haematology, Rockingham General Hospital, Rockingham, WA, Australia
| | - Rebecca Howman
- Department of Haematology, Sir Charles Gairdner Hospital Nedlands Australia
| | - Carolyn S Grove
- School of Biomedical Sciences, The University of Western Australia, Crawley, WA, Australia
- Department of Haematology, Royal Perth Hospital, Perth, WA, Australia
- Department of Haematology, Sir Charles Gairdner Hospital Nedlands Australia
| | | | - Michael F Leahy
- Department of Haematology, Royal Perth Hospital, Perth, WA, Australia
- PathWest Laboratory Medicine, Nedlands, WA, Australia
| | - Matthew D Linden
- School of Biomedical Sciences, The University of Western Australia, Crawley, WA, Australia
| | - Kathryn A Fuller
- School of Biomedical Sciences, The University of Western Australia, Crawley, WA, Australia
| | - Wendy N Erber
- School of Biomedical Sciences, The University of Western Australia, Crawley, WA, Australia
- PathWest Laboratory Medicine, Nedlands, WA, Australia
| | - Belinda B Guo
- School of Biomedical Sciences, The University of Western Australia, Crawley, WA, Australia
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Liu J, Liu S, Li D, Li H, Zhang F. Prevalence and Associations of Co-occurrence of NFE2L2 Mutations and Chromosome 3q26 Amplification in Lung Cancer. Glob Med Genet 2024; 11:150-158. [PMID: 38628662 PMCID: PMC11018393 DOI: 10.1055/s-0044-1786004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2024] Open
Abstract
Background NFE2L2 (nuclear factor erythroid-2-related factor-2) encodes a basic leucine zipper (bZIP) transcription factor and exhibits variations in various tumor types, including lung cancer. In this study, we comprehensively investigated the impact of simultaneous mutations on the survival of NFE2L2 -mutant lung cancer patients within specific subgroups. Methods A cohort of 1,103 lung cancer patients was analyzed using hybridization capture-based next-generation sequencing. Results The NFE2L2 gene had alterations in 3.0% (33/1,103) of lung cancer samples, including 1.5% (15/992) in adenocarcinoma and 16.2% (18/111) in squamous cell carcinoma. Thirty-four variations were found, mainly in exons 2 (27/34). New variations in exon 2 (p.D21H, p.V36_E45del, p.F37_E45del, p.R42P, p.E67Q, and p.L76_E78delinsQ) were identified. Some patients had copy number amplifications. Co-occurrence with TP53 (84.8%), CDKN2A (33.3%), KMT2B (33.3%), LRP1B (33.3%), and PIK3CA (27.3%) mutations was common. Variations of NFE2L2 displayed the tightest co-occurrence with IRF2 , TERC , ATR , ZMAT3 , and SOX2 ( p < 0.001). In The Cancer Genome Atlas Pulmonary Squamous Carcinoma project, patients with NFE2L2 variations and 3q26 amplification had longer median survival (63.59 vs. 32.04 months, p = 0.0459) and better overall survival. Conclusions NFE2L2 mutations display notable heterogeneity in lung cancer. The coexistence of NFE2L2 mutations and 3q26 amplification warrants in-depth exploration of their potential clinical implications and treatment approaches for affected patients.
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Affiliation(s)
- Jinfeng Liu
- Department of Thoracic Surgery, The First Hospital of Hebei Medical University, Shijiazhuang, China
| | - Sijie Liu
- Department of Thoracic Surgery, Beijing Aerospace General Hospital, Beijing, China
| | - Dan Li
- Department of General Surgery, Jingxing County Hospital of Hebei Province, Shijiazhuang, China
| | - Hongbin Li
- Department of Oncology, Rongcheng County People's Hospital, Baoding, China
| | - Fan Zhang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
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Shao B, Di L. Metastatic breast cancer with double heterozygosity for the BRCA1 and BRCA2 genes responding to olaparib: A case report. Oncol Lett 2024; 27:253. [PMID: 38646498 PMCID: PMC11027096 DOI: 10.3892/ol.2024.14387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 02/07/2023] [Indexed: 04/23/2024] Open
Abstract
Olaparib was the first poly ADP-ribose polymerase inhibitor approved for patients with cancer with mutations in either BRCA1 or BRCA2 in China. To the best of our knowledge, however, no study has described the efficacy of olaparib for patients with breast cancer with double mutations in BRCA1 and BRCA2. The present case report describes a patient with breast cancer with deleterious germline mutations in both BRCA1 and BRCA2. The 56-year-old patient with multiple metastatic breast cancer underwent breast cancer resection with 12 years interval between removal of the left and right breast. Germline mutations in both BRCA1 (S405X) and BRCA2 (W2990X) were identified by NGS. She received two cycles of chemotherapy with a combination of albumin-bound paclitaxel and capecitabine; the response was progressive disease. Subsequently, the patient was treated with a gradual dosage of decreasing olaparib (600 to 300 mg BID) for 6 months until grade 3 anemia could not be alleviated by giving erythropoietin and iron, and CT imaging showed a partial response (35% reduction). The patient then switched to exemestane therapy due to the continuous grade 3 anemia. In conclusion, the present study reported a female patient with double heterozygosity of BRCA1 and BRCA2 who benefited from olaparib monotherapy. Thus, olaparib may be a suitable treatment for such patients.
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Affiliation(s)
- Bin Shao
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Breast Oncology, Peking University Cancer Hospital and Institute, Beijing 100142, P.R. China
| | - Lijun Di
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Breast Oncology, Peking University Cancer Hospital and Institute, Beijing 100142, P.R. China
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Fitzpatrick AM, Huang M, Mohammad AF, Stephenson ST, Kamaleswaran R, Grunwell JR. Dysfunctional neutrophil type 1 interferon responses in preschool children with recurrent wheezing and IL-4-mediated aeroallergen sensitization. J Allergy Clin Immunol Glob 2024; 3:100229. [PMID: 38510797 PMCID: PMC10950716 DOI: 10.1016/j.jacig.2024.100229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 11/25/2023] [Accepted: 12/24/2023] [Indexed: 03/22/2024]
Abstract
Background The innate mechanisms associated with viral exacerbations in preschool children with recurrent wheezing are not understood. Objective We sought to assess differential gene expression in blood neutrophils from preschool children with recurrent wheezing, stratified by aeroallergen sensitization, at baseline and after exposure to polyinosinic:polycytidylic acid (poly(I:C)) and also to examine whether poly(I:C)-stimulated blood neutrophils influenced airway epithelial gene expression. Methods Blood neutrophils were purified and cultured overnight with poly(I:C) and underwent next-generation sequencing with Reactome pathway analysis. Primary human small airway epithelial cells were treated with poly(I:C)-treated neutrophil culture supernatants and were analyzed for type 1 interferon gene expression with a targeted array. Symptoms and exacerbations were assessed in participants over 12 months. Results A total of 436 genes were differently expressed in neutrophils from children with versus without aeroallergen sensitization at baseline, with significant downregulation of type 1 interferons. These type 1 interferons were significantly upregulated in sensitized children after poly(I:C) stimulation. Confirmatory experiments demonstrated similar upregulation of type 1 interferons in IL-4-treated neutrophils stimulated with poly(I:C). Poly(I:C)-treated neutrophil supernatants from children with aeroallergen sensitization also induced a type 1 interferon response in epithelial cells. Children with aeroallergen sensitization also had higher symptom scores during exacerbations, and these symptom differences persisted for 3 days after prednisolone treatment. Conclusions Type 1 interferon responses are dysregulated in preschool children with aeroallergen sensitization, which is in turn associated with exacerbation severity. Given the importance of type 1 interferon signaling in viral resolution, additional studies of neutrophil type 1 interferon responses are needed in this population.
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Affiliation(s)
- Anne M. Fitzpatrick
- Department of Pediatrics, Emory University, Atlanta, Ga
- Division of Pulmonary Medicine, Children’s Healthcare of Atlanta, Atlanta, Ga
| | - Min Huang
- Department of Biomedical Informatics, Emory University, Atlanta, Ga
| | | | | | | | - Jocelyn R. Grunwell
- Department of Pediatrics, Emory University, Atlanta, Ga
- Division of Critical Care Medicine, Children’s Healthcare of Atlanta, Atlanta, Ga
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Eum HH, Jeong D, Kim N, Jo A, Na M, Kang H, Hong Y, Kong JS, Jeong GH, Yoo SA, Lee HO. Single-cell RNA sequencing reveals myeloid and T cell co-stimulation mediated by IL-7 anti-cancer immunotherapy. Br J Cancer 2024; 130:1388-1401. [PMID: 38424167 PMCID: PMC11014989 DOI: 10.1038/s41416-024-02617-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 02/03/2024] [Accepted: 02/08/2024] [Indexed: 03/02/2024] Open
Abstract
BACKGROUND Immune checkpoint inhibitors unleash inhibitory signals on T cells conferred by tumors and surrounding stromal cells. Despite the clinical efficacy of checkpoint inhibitors, the lack of target expression and persistence of immunosuppressive cells limit the pervasive effectiveness of the therapy. These limitations may be overcome by alternative approaches that co-stimulate T cells and the immune microenvironment. METHODS We analyzed single-cell RNA sequencing data from multiple human cancers and a mouse tumor transplant model to discover the pleiotropic expression of the Interleukin 7 (IL-7) receptor on T cells, macrophages, and dendritic cells. RESULTS Our experiment on the mouse model demonstrated that recombinant IL-7 therapy induces tumor regression, expansion of effector CD8 T cells, and pro-inflammatory activation of macrophages. Moreover, spatial transcriptomic data support immunostimulatory interactions between macrophages and T cells. CONCLUSION These results indicate that IL-7 therapy induces anti-tumor immunity by activating T cells and pro-inflammatory myeloid cells, which may have diverse therapeutic applicability.
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Affiliation(s)
- Hye Hyeon Eum
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, 06591, Republic of Korea
- Department of Biomedicine and Health Sciences, Graduate School, The Catholic University of Korea, Seoul, 06591, Republic of Korea
| | - Dasom Jeong
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, 06591, Republic of Korea
- Department of Biomedicine and Health Sciences, Graduate School, The Catholic University of Korea, Seoul, 06591, Republic of Korea
| | - Nayoung Kim
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, 06591, Republic of Korea
- Department of Biomedicine and Health Sciences, Graduate School, The Catholic University of Korea, Seoul, 06591, Republic of Korea
| | - Areum Jo
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, 06591, Republic of Korea
- Department of Biomedicine and Health Sciences, Graduate School, The Catholic University of Korea, Seoul, 06591, Republic of Korea
| | - Minsu Na
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, 06591, Republic of Korea
- Department of Biomedicine and Health Sciences, Graduate School, The Catholic University of Korea, Seoul, 06591, Republic of Korea
| | - Huiram Kang
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, 06591, Republic of Korea
- Department of Biomedicine and Health Sciences, Graduate School, The Catholic University of Korea, Seoul, 06591, Republic of Korea
| | - Yourae Hong
- Digestive Oncology, Department of Oncology, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Jin-Sun Kong
- Department of Biomedicine and Health Sciences, Graduate School, The Catholic University of Korea, Seoul, 06591, Republic of Korea
- Center for Integrative Rheumatoid Transcriptomics and Dynamics, College of Medicine, The Catholic University of Korea, Seoul, 06591, Republic of Korea
| | - Gi Heon Jeong
- Department of Biomedicine and Health Sciences, Graduate School, The Catholic University of Korea, Seoul, 06591, Republic of Korea
- Center for Integrative Rheumatoid Transcriptomics and Dynamics, College of Medicine, The Catholic University of Korea, Seoul, 06591, Republic of Korea
| | - Seung-Ah Yoo
- Department of Biomedicine and Health Sciences, Graduate School, The Catholic University of Korea, Seoul, 06591, Republic of Korea
- Center for Integrative Rheumatoid Transcriptomics and Dynamics, College of Medicine, The Catholic University of Korea, Seoul, 06591, Republic of Korea
| | - Hae-Ock Lee
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, 06591, Republic of Korea.
- Department of Biomedicine and Health Sciences, Graduate School, The Catholic University of Korea, Seoul, 06591, Republic of Korea.
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Flory A, Ruiz-Perez CA, Clavere-Graciette AG, Rafalko JM, O'Kell AL, Flesner BK, McLennan LM, Hicks SC, Nakashe P, Phelps-Dunn A, DiMarzio LR, Warren CD, Cohen TA, Chibuk J, Chorny I, Grosu DS, Tsui DWY, Tynan JA, Kruglyak KM. Clinical validation of a blood-based liquid biopsy test integrating cell-free DNA quantification and next-generation sequencing for cancer screening in dogs. J Am Vet Med Assoc 2024; 262:665-673. [PMID: 38324993 DOI: 10.2460/javma.23.10.0564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 01/05/2024] [Indexed: 02/09/2024]
Abstract
OBJECTIVE To validate the performance of a novel, integrated test for canine cancer screening that combines cell-free DNA quantification with next-generation sequencing (NGS) analysis. SAMPLE Retrospective data from a total of 1,947 cancer-diagnosed and presumably cancer-free dogs were used to validate test performance for the detection of 7 predefined cancer types (lymphoma, hemangiosarcoma, osteosarcoma, leukemia, histiocytic sarcoma, primary lung tumors, and urothelial carcinoma), using independent training and testing sets. METHODS Cell-free DNA quantification data from all samples were analyzed using a proprietary machine learning algorithm to determine a Cancer Probability Index (High, Moderate, or Low). High and Low Probability of Cancer were final result classifications. Moderate cases were additionally analyzed by NGS to arrive at a final classification of High Probability of Cancer (Cancer Signal Detected) or Low Probability of Cancer (Cancer Signal Not Detected). RESULTS Of the 595 dogs in the testing set, 89% (n = 530) received a High or Low Probability result based on the machine learning algorithm; 11% (65) were Moderate Probability, and NGS results were used to assign a final classification. Overall, 87 of 122 dogs with the 7 predefined cancer types were classified as High Probability and 467 of 473 presumably cancer-free dogs were classified as Low Probability, corresponding to a sensitivity of 71.3% for the predefined cancer types at a specificity of 98.7%. CLINICAL RELEVANCE This integrated test offers a novel option to screen for cancer types that may be difficult to detect by physical examination at a dog's wellness visit.
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Affiliation(s)
- Andi Flory
- 1Medical and Clinical Affairs, PetDx, La Jolla, CA
| | | | | | | | | | | | | | | | | | | | | | | | - Todd A Cohen
- 1Medical and Clinical Affairs, PetDx, La Jolla, CA
| | - Jason Chibuk
- 1Medical and Clinical Affairs, PetDx, La Jolla, CA
| | - Ilya Chorny
- 2Information Technology, PetDx, La Jolla, CA
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Nascimento FF, Mehta SR, Little SJ, Volz EM. Assessing transmission attribution risk from simulated sequencing data in HIV molecular epidemiology. AIDS 2024; 38:865-873. [PMID: 38126363 PMCID: PMC10994139 DOI: 10.1097/qad.0000000000003820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 12/08/2023] [Accepted: 12/14/2023] [Indexed: 12/23/2023]
Abstract
BACKGROUND HIV molecular epidemiology (ME) is the analysis of sequence data together with individual-level clinical, demographic, and behavioral data to understand HIV epidemiology. The use of ME has raised concerns regarding identification of the putative source in direct transmission events. This could result in harm ranging from stigma to criminal prosecution in some jurisdictions. Here we assessed the risks of ME using simulated HIV genetic sequencing data. METHODS We simulated social networks of men-who-have-sex-with-men, calibrating the simulations to data from San Diego. We used these networks to simulate consensus and next-generation sequence (NGS) data to evaluate the risks of identifying direct transmissions using different HIV sequence lengths, and population sampling depths. To identify the source of transmissions, we calculated infector probability and used phyloscanner software for the analysis of consensus and NGS data, respectively. RESULTS Consensus sequence analyses showed that the risk of correctly inferring the source (direct transmission) within identified transmission pairs was very small and independent of sampling depth. Alternatively, NGS analyses showed that identification of the source of a transmission was very accurate, but only for 6.5% of inferred pairs. False positive transmissions were also observed, where one or more unobserved intermediaries were present when compared to the true network. CONCLUSION Source attribution using consensus sequences rarely infers direct transmission pairs with high confidence but is still useful for population studies. In contrast, source attribution using NGS data was much more accurate in identifying direct transmission pairs, but for only a small percentage of transmission pairs analyzed.
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Affiliation(s)
- Fabrícia F. Nascimento
- MRC Centre for Global Infectious Disease Analysis and the Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Sanjay R. Mehta
- Division of Infectious Diseases, University of California San Diego, San Diego, CA, USA
| | - Susan J. Little
- Division of Infectious Diseases, University of California San Diego, San Diego, CA, USA
| | - Erik M. Volz
- MRC Centre for Global Infectious Disease Analysis and the Department of Infectious Disease Epidemiology, Imperial College London, London, UK
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Nie Z, Zeng K, Yan Q, Liu Y, Bian Y, Zhu J, Guo Z, He F, Shi H, Guo Y. The Relationship Between Gene Mutations and the Clinicopathological Features and Prognosis of Gastric Cancer. Int J Surg Pathol 2024; 32:486-495. [PMID: 37545327 DOI: 10.1177/10668969231188421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Current treatments for gastric cancer (GC) are suboptimal. Potential therapeutic targets for GC were screened using next-generation sequencing. We examined many mutation genes linked to GC, including TP53 (60%), PIK3CA (19%), LRP1B (13%), and ERBB2 (12%), ARID1A (9%), KMT2C (9%), and KRAS (7%). The KMT2C, KRAS, CDK6, and ARID1A wild-type genes were dominant in diffuse-type GC (P < .05), but mutations did not influence prognosis. Patients with APC (6%) and CDH1 (8%) wild-type GC presented with vascular invasion (P < .05). Patients with ATR (2%) wild-type GC were prone to lymph node metastasis (P < .05). Patients with ARID1A (9%) wild-type GC had reduced programmed death ligand 1 expression (<1, P < .05). We found that patients who received chemotherapy had a better prognosis than those who did not (although there was no statistical difference), with platinum-based group having better prognosis and uracil combined with paclitaxel group having worse prognosis.
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Affiliation(s)
- Zunzhen Nie
- Department of Pathology, Xi'an Daxing Hospital, Xi'an, China
| | - Kaixuan Zeng
- Precision Medical Research Institute, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Qingguo Yan
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Medicine, Northwest University, Xi'an, China
| | - Yuangang Liu
- Department of Pathology, Xi'an Daxing Hospital, Xi'an, China
| | - Yawei Bian
- Department of Pathology, Xi'an Daxing Hospital, Xi'an, China
| | - Jin Zhu
- Department of Pathology, Xi'an Daxing Hospital, Xi'an, China
| | - Zhenzhen Guo
- Department III of General Surgery, Xi'an Daxing Hospital, Xi'an, China
| | - Furong He
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Medicine, Northwest University, Xi'an, China
| | - Hai Shi
- Department of Gastrointestinal Surgery, Xi'an Daxing Hospital, Xi'an, China
| | - Ying Guo
- Department of Pathology, Xi'an Daxing Hospital, Xi'an, China
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Medicine, Northwest University, Xi'an, China
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Mhanna V, Barennes P, Vantomme H, Fourcade G, Coatnoan N, Six A, Klatzmann D, Mariotti-Ferrandiz E. Enhancing comparative T cell receptor repertoire analysis in small biological samples through pooling homologous cell samples from multiple mice. Cell Rep Methods 2024; 4:100753. [PMID: 38614088 DOI: 10.1016/j.crmeth.2024.100753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 01/28/2024] [Accepted: 03/19/2024] [Indexed: 04/15/2024]
Abstract
Accurate characterization and comparison of T cell receptor (TCR) repertoires from small biological samples present significant challenges. The main challenge is the low material input, which compromises the quality of bulk sequencing and hinders the recovery of sufficient TCR sequences for robust analyses. We aimed to address this limitation by implementing a strategic approach to pool homologous biological samples. Our findings demonstrate that such pooling indeed enhances the TCR repertoire coverage, particularly for cell subsets of constrained sizes, and enables accurate comparisons of TCR repertoires at different levels of complexity across T cell subsets with different sizes. This methodology holds promise for advancing our understanding of T cell repertoires in scenarios where sample size constraints are a prevailing concern.
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Affiliation(s)
- Vanessa Mhanna
- Sorbonne Université, INSERM, Immunology-Immunopathology-Immunotherapy (i3), 75005 Paris, France; AP-HP, Hôpital Pitié-Salpêtrière, Clinical Investigation Center for Biotherapies (CIC-BTi) and Immunology-Inflammation-Infectiology and Dermatology Department (3iD), Paris, France
| | - Pierre Barennes
- Sorbonne Université, INSERM, Immunology-Immunopathology-Immunotherapy (i3), 75005 Paris, France; AP-HP, Hôpital Pitié-Salpêtrière, Clinical Investigation Center for Biotherapies (CIC-BTi) and Immunology-Inflammation-Infectiology and Dermatology Department (3iD), Paris, France
| | - Hélène Vantomme
- AP-HP, Hôpital Pitié-Salpêtrière, Clinical Investigation Center for Biotherapies (CIC-BTi) and Immunology-Inflammation-Infectiology and Dermatology Department (3iD), Paris, France
| | - Gwladys Fourcade
- Sorbonne Université, INSERM, Immunology-Immunopathology-Immunotherapy (i3), 75005 Paris, France
| | - Nicolas Coatnoan
- AP-HP, Hôpital Pitié-Salpêtrière, Clinical Investigation Center for Biotherapies (CIC-BTi) and Immunology-Inflammation-Infectiology and Dermatology Department (3iD), Paris, France
| | - Adrien Six
- Sorbonne Université, INSERM, Immunology-Immunopathology-Immunotherapy (i3), 75005 Paris, France
| | - David Klatzmann
- Sorbonne Université, INSERM, Immunology-Immunopathology-Immunotherapy (i3), 75005 Paris, France; AP-HP, Hôpital Pitié-Salpêtrière, Clinical Investigation Center for Biotherapies (CIC-BTi) and Immunology-Inflammation-Infectiology and Dermatology Department (3iD), Paris, France
| | - Encarnita Mariotti-Ferrandiz
- Sorbonne Université, INSERM, Immunology-Immunopathology-Immunotherapy (i3), 75005 Paris, France; Institut Universitaire de France, France.
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11
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Vittone J, Gill D, Goldsmith A, Klein EA, Karlitz JJ. A multi-cancer early detection blood test using machine learning detects early-stage cancers lacking USPSTF-recommended screening. NPJ Precis Oncol 2024; 8:91. [PMID: 38632333 PMCID: PMC11024170 DOI: 10.1038/s41698-024-00568-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 03/15/2024] [Indexed: 04/19/2024] Open
Abstract
US Preventive Services Task Force (USPSTF) guidelines recommend single-cancer screening for select cancers (e.g., breast, cervical, colorectal, lung). Advances in genome sequencing and machine learning have facilitated the development of blood-based multi-cancer early detection (MCED) tests intended to complement single-cancer screening. MCED tests can interrogate circulating cell-free DNA to detect a shared cancer signal across multiple tumor types. We report real-world experience with an MCED test that detected cancer signals in three individuals subsequently diagnosed with cancers of the ovary, kidney, and head/neck that lack USPSTF-recommended screening. These cases illustrate the potential of MCED tests to detect early-stage cancers amenable to cure.
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Affiliation(s)
| | - David Gill
- Intermountain Healthcare, Salt Lake City, UT, USA
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12
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Trégouët DA, Pierre-Emmanuel M. Next Generation Sequencing strategies in venous thromboembolism: in whom and for what purpose ? J Thromb Haemost 2024:S1538-7836(24)00218-6. [PMID: 38641321 DOI: 10.1016/j.jtha.2024.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 04/04/2024] [Accepted: 04/05/2024] [Indexed: 04/21/2024]
Abstract
This invited review follows the oral presentation "To Sequence or Not to Sequence, That Is Not the Question; But "When, Who, Which and What For?" Is " given during the State Of the Art session Translational Genomics in Thrombosis: From OMICs to Clinics" of the ISTH 2023 congress. Emphasizing the power of next-generation sequencing technologies and the diverse strategies associated with DNA variant analysis, this review highlights the unresolved questions and challenges in their implementation both for the clinical diagnosis of venous thromboembolism and in translational research.
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Affiliation(s)
- David-Alexandre Trégouët
- Univ. Bordeaux, Inserm, Bordeaux Population Health Research Center, UMR 1219, F-33000 Bordeaux, France
| | - Morange Pierre-Emmanuel
- Cardiovascular and Nutrition Research Center (C2VN), INSERM, INRAE, Aix-Marseille University, Marseille, France
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13
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Osborn LJ, Fissel J, Gomez S, Mestas J, Flores-Vazquez J, Lee J, Hakimjavadi H, Costales C, Dien Bard J. Development of an automated amplicon-based next-generation sequencing pipeline for rapid detection of bacteria and fungi directly from clinical specimens. J Clin Microbiol 2024:e0174923. [PMID: 38624235 DOI: 10.1128/jcm.01749-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 03/23/2024] [Indexed: 04/17/2024] Open
Abstract
The timely identification of microbial pathogens is essential to guide targeted antimicrobial therapy and ultimately, successful treatment of an infection. However, the yield of standard microbiology testing (SMT) is directly related to the duration of antecedent antimicrobial therapy as SMT culture methods are dependent on the recovery of viable organisms, the fastidious nature of certain pathogens, and other pre-analytic factors. In the last decade, metagenomic next-generation sequencing (mNGS) has been successfully utilized as a diagnostic tool for various applications within the clinical laboratory. However, mNGS is resource, time, and labor-intensive-requiring extensive laborious preliminary benchwork, followed by complex bioinformatic analysis. We aimed to address these shortcomings by developing a largely Automated targeted Metagenomic next-generation sequencing (tmNGS) PipeLine for rapId inFectIous disEase Diagnosis (AMPLIFIED) to detect bacteria and fungi directly from clinical specimens. Therefore, AMPLIFIED may serve as an adjunctive approach to complement SMT. This tmNGS pipeline requires less than 1 hour of hands-on time before sequencing and less than 2 hours of total processing time, including bioinformatic analysis. We performed tmNGS on 50 clinical specimens with concomitant cultures to assess feasibility and performance in the hospital laboratory. Of the 50 specimens, 34 (68%) were from true clinical infections. Specimens from cases of true infection were more often tmNGS positive compared to those from the non-infected group (82.4% vs 43.8%, respectively, P = 0.0087). Overall, the clinical sensitivity of AMPLIFIED was 54.6% with 85.7% specificity, equating to 70.6% and 75% negative and positive predictive values, respectively. AMPLIFIED represents a rapid supplementary approach to SMT; the typical time from specimen receipt to identification of potential pathogens by AMPLIFIED is roughly 24 hours which is markedly faster than the days, weeks, and months required to recover bacterial, fungal, and mycobacterial pathogens by culture, respectively. IMPORTANCE To our knowledge, this represents the first application of an automated sequencing and bioinformatics pipeline in an exclusively pediatric population. Next-generation sequencing is time-consuming, labor-intensive, and requires experienced personnel; perhaps contributing to hesitancy among clinical laboratories to adopt such a test. Here, we report a strong case for use by removing these barriers through near-total automation of our sequencing pipeline.
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Affiliation(s)
- Lucas J Osborn
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California, USA
| | - John Fissel
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California, USA
| | - Samantha Gomez
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California, USA
| | - Javier Mestas
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California, USA
| | - Jessica Flores-Vazquez
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California, USA
| | - Jaehyeon Lee
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California, USA
- Department of Laboratory Medicine, Jeonbuk National University Medical School and Hospital, Jeonju, Jeollabukdo, South Korea
| | - Hesamedin Hakimjavadi
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California, USA
| | - Cristina Costales
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California, USA
- Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Jennifer Dien Bard
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California, USA
- Keck School of Medicine, University of Southern California, Los Angeles, California, USA
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14
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Shelton WJ, Mathews AP, Aljiboori K, Nix JS, Gokden M, Rodriguez A. A rare case of atypical intradural extramedullary glioblastoma diagnosed utilizing next-generation sequencing and methylation profiling: illustrative case. J Neurosurg Case Lessons 2024; 7:CASE24103. [PMID: 38621302 PMCID: PMC11023011 DOI: 10.3171/case24103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Accepted: 02/29/2024] [Indexed: 04/17/2024]
Abstract
BACKGROUND Primary spinal cord tumors, especially primary spinal cord glioblastoma multiforme (PSC-GBM), are exceptionally rare, accounting for less than 1.5% of all spinal tumors. Their infrequency and aggressive yet atypical presentation make diagnosis challenging. In uncertain cases, a surgical approach for tissue diagnosis is often optimal. OBSERVATIONS A 76-year-old male presented with a rapidly progressing clinical history marked by worsening extremity weakness, urinary retention, and periodic fecal incontinence alongside diffuse changes on neuraxis imaging. The patient, in whom subacute polyneuropathy was initially diagnosed, received multiple rounds of steroids and intravenous immunoglobulin without clinical improvement. Histopathological review of the biopsy tissue yielded an initial diagnosis of spindle cell neoplasm. Next-generation sequencing (NGS) is done routinely on all neuropathology specimens at the authors' institution, and methylation profiling is pursued in difficult cases. Ultimately, NGS and methylation profiling results were essential to an integrated final diagnosis of GBM. LESSONS PSC-GBM is a rare but highly aggressive occurrence of this tumor. Prolonged back pain, rapid neurological decline, and imaging changes warrant the consideration of lesional biopsy for precise disease characterization. In inconclusive cases, NGS has proved invaluable for clinical clarification and diagnosis, underscoring its importance for integrated diagnoses in guiding appropriate treatment strategies.
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Affiliation(s)
| | | | | | - J. Stephen Nix
- Pathology, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Murat Gokden
- Pathology, University of Arkansas for Medical Sciences, Little Rock, Arkansas
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15
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Lim FS, González-Cabrera J, Keilwagen J, Kleespies RG, Jehle JA, Wennmann JT. Advancing pathogen surveillance by nanopore sequencing and genotype characterization of Acheta domesticus densovirus in mass-reared house crickets. Sci Rep 2024; 14:8525. [PMID: 38609404 PMCID: PMC11014933 DOI: 10.1038/s41598-024-58768-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 04/03/2024] [Indexed: 04/14/2024] Open
Abstract
Rapid and reliable detection of pathogens is crucial to complement the growing industry of mass-reared insects, in order to safeguard the insect colonies from outbreak of diseases, which may cause significant economic loss. Current diagnostic methods are mainly based on conventional PCR and microscopic examination, requiring prior knowledge of disease symptoms and are limited to identifying known pathogens. Here, we present a rapid nanopore-based metagenomics approach for detecting entomopathogens from the European house cricket (Acheta domesticus). In this study, the Acheta domesticus densovirus (AdDV) was detected from diseased individuals using solely Nanopore sequencing. Virus reads and genome assemblies were obtained within twenty-four hours after sequencing. Subsequently, due to the length of the Nanopore reads, it was possible to reconstruct significantly large parts or even the entire AdDV genome to conduct studies for genotype identification. Variant analysis indicated the presence of three AdDV genotypes within the same house cricket population, with association to the vital status of the diseased crickets. This contrast provided compelling evidence for the existence of non-lethal AdDV genotypes. These findings demonstrated nanopore-based metagenomics sequencing as a powerful addition to the diagnostic tool kit for routine pathogen surveillance and diagnosis in the insect rearing industry.
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Affiliation(s)
- Fang Shiang Lim
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Biological Control, Schwabenheimer Str. 101, 69221, Dossenheim, Germany
- Department of Genetics and Institute BIOTECMED, Universitat de València, Dr Moliner 50, 46100, Burjassot, Spain
| | - Joel González-Cabrera
- Department of Genetics and Institute BIOTECMED, Universitat de València, Dr Moliner 50, 46100, Burjassot, Spain
| | - Jens Keilwagen
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for the Safety of Biotechnological Processes in Plants, Erwin-Baur-Str. 27, 06484, Quedlinburg, Germany
| | - Regina G Kleespies
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Biological Control, Schwabenheimer Str. 101, 69221, Dossenheim, Germany
| | - Johannes A Jehle
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Biological Control, Schwabenheimer Str. 101, 69221, Dossenheim, Germany
| | - Jörg T Wennmann
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Biological Control, Schwabenheimer Str. 101, 69221, Dossenheim, Germany.
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16
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Dzofou Ngoumelah D, Heggeset TMB, Haugen T, Sulheim S, Wentzel A, Harnisch F, Kretzschmar J. Author Correction: Effect of model methanogens on the electrochemical activity, stability, and microbial community structure of Geobacter spp. dominated biofilm anodes. NPJ Biofilms Microbiomes 2024; 10:41. [PMID: 38609420 PMCID: PMC11014964 DOI: 10.1038/s41522-024-00513-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2024] Open
Affiliation(s)
- Daniel Dzofou Ngoumelah
- DBFZ Deutsches Biomasseforschungszentrum gemeinnützige GmbH (German Biomass Research Centre), Department of Biochemical Conversion, 04347, Leipzig, Germany
| | | | - Tone Haugen
- SINTEF Industry, Department of Biotechnology and Nanomedicine, 7034, Trondheim, Norway
| | - Snorre Sulheim
- SINTEF Industry, Department of Biotechnology and Nanomedicine, 7034, Trondheim, Norway
| | - Alexander Wentzel
- SINTEF Industry, Department of Biotechnology and Nanomedicine, 7034, Trondheim, Norway
| | - Falk Harnisch
- Helmholtz Centre for Environmental Research - UFZ, Department of Microbial Biotechnology, 04318, Leipzig, Germany
| | - Jörg Kretzschmar
- DBFZ Deutsches Biomasseforschungszentrum gemeinnützige GmbH (German Biomass Research Centre), Department of Biochemical Conversion, 04347, Leipzig, Germany.
- Zittau/Görlitz University of Applied Sciences, Faculty of Natural and Environmental Sciences, 02763, Zittau, Germany.
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17
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Park SY, Faraci G, Ward P, Lee HY. Utilizing cost-effective portable equipment to enhance COVID-19 variant tracking both on-site and at a large scale. J Clin Microbiol 2024; 62:e0155823. [PMID: 38415638 PMCID: PMC11005371 DOI: 10.1128/jcm.01558-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 02/12/2024] [Indexed: 02/29/2024] Open
Abstract
Despite optimistic predictions on the eventual end of COVID-19 (Coronavirus Disease 2019), caution is necessary regarding the emergence of new variants to sustain a positive outlook and effectively address any potential future outbreaks. However, ongoing efforts to track COVID-19 variants are concentrated in developed countries and unique social practices and remote habitats of indigenous peoples present additional challenges. By combining small-sized equipment that is easily accessible and inexpensive, we performed SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) whole genome sequencing and measured the sample-to-answer time and accuracy of this portable variant tracking tool. Our portable design determined the variant of SARS-CoV-2 in an infected individual within 9 hours and 15 minutes without external power or internet connection, surpassing the speed of previous portable tools. It took only 16 minutes to complete sequencing run, whole genome assembly, and lineage determination using a single standalone laptop. We then demonstrated the capability to produce 289 SARS-CoV-2 whole genome sequences in a single portable sequencing run, representing a significant improvement over an existing throughput of 96 sequences per run. We verified the accuracy of portable sequencing by comparison with two other independent sequencing methods. We showed that our high-throughput data consistently represented the circulating variants in Los Angeles, United States, when compared with publicly available sequences. Our scheme is designed to be flexible, rapid, and accurate, making it a valuable tool for large-scale surveillance operations in low- and middle-income countries as well as targeted surveys for vulnerable populations in remote locations.IMPORTANCEThere have been significant efforts to track COVID-19 (Coronavirus Disease 2019) variants, accumulating over 15 million SARS-CoV-2 sequences as of 2023. However, the distribution of global survey data is highly skewed, with nearly half of all countries having inadequate or low levels of genomic surveillance. In addition, indigenous peoples face more severe threats from COVID-19, due to their generally remote residence and unique social practices. Cost-effective portable sequencing tools have been used to investigate Ebola and Zika outbreaks. However, these tools have a sample-to-answer time of around 24 hours and require an internet connection for data transfer to an off-site cloud server. In our study, we rapidly determined COVID-19 variants using only small and inexpensive equipment, with a completion time of 9 hours and 15 minutes. Furthermore, we produced 289 near-full-length SARS-CoV-2 genome sequences from a single portable Nanopore sequencing run, representing a threefold increase in throughput compared with existing Nanopore sequencing methods.
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Affiliation(s)
- Sung Yong Park
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Gina Faraci
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Pamela Ward
- Department of Clinical Pathology, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Ha Youn Lee
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
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18
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Cohen ASA, Berrios CD, Zion TN, Barrett CM, Moore R, Boillat E, Belden B, Farrow EG, Thiffault I, Zuccarelli BD, Pastinen T. Genomic Answers for Kids: Toward more equitable access to genomic testing for rare diseases in rural populations. Am J Hum Genet 2024:S0002-9297(24)00114-9. [PMID: 38636509 DOI: 10.1016/j.ajhg.2024.03.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 03/26/2024] [Accepted: 03/27/2024] [Indexed: 04/20/2024] Open
Abstract
Next-generation sequencing has revolutionized the speed of rare disease (RD) diagnoses. While clinical exome and genome sequencing represent an effective tool for many RD diagnoses, there is room to further improve the diagnostic odyssey of many RD patients. One recognizable intervention lies in increasing equitable access to genomic testing. Rural communities represent a significant portion of underserved and underrepresented individuals facing additional barriers to diagnosis and treatment. Primary care providers (PCPs) at local clinics, though sometimes suspicious of a potential benefit of genetic testing for their patients, have significant constraints in pursuing it themselves and rely on referrals to specialists. Yet, these referrals are typically followed by long waitlists and significant delays in clinical assessment, insurance clearance, testing, and initiation of diagnosis-informed care management. Not only is this process time intensive, but it also often requires multiple visits to urban medical centers for which distance may be a significant barrier to rural families. Therefore, providing early, "direct-to-provider" (DTP) local access to unrestrictive genomic testing is likely to help speed up diagnostic times and access to care for RD patients in rural communities. In a pilot study with a PCP clinic in rural Kansas, we observed a minimum 5.5 months shortening of time to diagnosis through the DTP exome sequencing program as compared to rural patients receiving genetic testing through the "traditional" PCP-referral-to-specialist scheme. We share our experience to encourage future partnerships beyond our center. Our efforts represent just one step in fostering greater diversity and equity in genomic studies.
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Affiliation(s)
- Ana S A Cohen
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO 64108, USA; Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO 64108, USA; UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO 64108, USA.
| | - Courtney D Berrios
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO 64108, USA; UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO 64108, USA
| | - Tricia N Zion
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO 64108, USA
| | - Cassandra M Barrett
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO 64108, USA
| | - Riley Moore
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO 64108, USA
| | - Emelia Boillat
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO 64108, USA
| | - Bradley Belden
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO 64108, USA
| | - Emily G Farrow
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO 64108, USA; Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO 64108, USA; UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO 64108, USA
| | - Isabelle Thiffault
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO 64108, USA; Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO 64108, USA; UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO 64108, USA
| | - Britton D Zuccarelli
- Salina Pediatric Care, Salina Regional Health Center, Salina, KS 67401, USA; Department of Pediatrics, University of Kansas School of Medicine - Salina Campus, Salina, KS 67401, USA
| | - Tomi Pastinen
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO 64108, USA; UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO 64108, USA; Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO 64108, USA
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19
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Bouzalas I, Apostolidi ED, Scalas D, Davidopoulou E, Chassalevris T, Rosati S, Colitti B. A Combined Approach for the Characterization of Small Ruminant Lentivirus Strains Circulating in the Islands and Mainland of Greece. Animals (Basel) 2024; 14:1119. [PMID: 38612358 PMCID: PMC11010947 DOI: 10.3390/ani14071119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 04/04/2024] [Accepted: 04/05/2024] [Indexed: 04/14/2024] Open
Abstract
Small ruminant lentiviruses are a group of viruses infecting goat and sheep worldwide. These viruses exhibit an extraordinary degree of genetic and antigenic variability that severely influence in vivo and in vitro features, as well as diagnostic test results. Small ruminant farming is the most important animal farming business in Greece, with a high impact on the Greek primary economy. Although SRLV infection and its impact on animal production are well established in the country, little is known about the circulating SRLV strains and their prevalence. The aim of this study was to characterize SRLVs circulating in Greece with a combined serological and molecular approach, using the bulk milk matrix collected from 60 farms in different municipalities. This study allowed us to estimate a seroprevalence of around 52% at the herd level. The B1, B2 and A3 subtypes and a novel A viral cluster were identified. Moreover, the amplicon sequencing method allowed us to identify more than one viral subtype in a sample. These results again confirm the high variability of these viruses and highlight the importance of the constant monitoring of viral evolution, in particular in antigens of diagnostic interest.
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Affiliation(s)
- Ilias Bouzalas
- Hellenic Agricultural Organization—DEMETER, Veterinary Research Institute, Campus of Thermi, 57001 Thessaloniki, Greece; (I.B.); (E.D.A.); (T.C.)
| | - Evangelia D. Apostolidi
- Hellenic Agricultural Organization—DEMETER, Veterinary Research Institute, Campus of Thermi, 57001 Thessaloniki, Greece; (I.B.); (E.D.A.); (T.C.)
| | - Daniela Scalas
- Department of Veterinary Sciences, University of Turin, L. Braccini 2, 10095 Torino, Italy; (D.S.); (S.R.)
| | | | - Taxiarchis Chassalevris
- Hellenic Agricultural Organization—DEMETER, Veterinary Research Institute, Campus of Thermi, 57001 Thessaloniki, Greece; (I.B.); (E.D.A.); (T.C.)
| | - Sergio Rosati
- Department of Veterinary Sciences, University of Turin, L. Braccini 2, 10095 Torino, Italy; (D.S.); (S.R.)
| | - Barbara Colitti
- Department of Veterinary Sciences, University of Turin, L. Braccini 2, 10095 Torino, Italy; (D.S.); (S.R.)
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20
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Zhang Z, Huang Y, Gu H, Zhao L, Zhao B. Efficacy of befotertinib in non-small cell lung cancer harboring uncommon compound EGFR mutations G719X and S768I: a case report. Front Oncol 2024; 14:1370666. [PMID: 38638860 PMCID: PMC11024360 DOI: 10.3389/fonc.2024.1370666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 03/25/2024] [Indexed: 04/20/2024] Open
Abstract
The discovery of epidermal growth factor receptor (EGFR) somatic mutations and the availability of tyrosine kinase inhibitors (TKIs) as targeted therapies have transformed the treatment landscape for advanced non-small cell lung cancer (NSCLC). p.G719X and p.S768I mutations, often present in the form of complex mutations, are considered rare. This study firstly reported the treatment outcome of a locally advanced unresectable NSCLC patient with a rare complex EGFR p.G719X/p.S768I mutations who received befotertinib. After treatment, the patient achieved partial response (PR), and no severe adverse events were observed. This case report supported befotertinib as a promising treatment option for advanced NSCLC patients with the rare p.G719X/p.S768I complex mutations.
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Affiliation(s)
| | | | | | | | - Baiqin Zhao
- Department of Thoracic Surgery, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
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21
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Zeng N, Gao W, Chen Z, Chong JY, Lee SY, Xu G. The complete chloroplast genome sequence and phylogenetic analysis of Strobilanthes dalzielii (W.W.Sm.) Benoist 1935 (Acanthaceae). Mitochondrial DNA B Resour 2024; 9:465-469. [PMID: 38591052 PMCID: PMC11000602 DOI: 10.1080/23802359.2024.2316069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 02/03/2024] [Indexed: 04/10/2024] Open
Abstract
Strobilanthes dalzielii of Acanthaceae is an herb species with potentially extensive applications for its pharmaceutical and ornamental values. Due to taxonomic complications and limited genetic information, the structural characteristics, and phylogenetic relationships of the S. dalzielii chloroplast genome were assembled and characterized here for the first time. The complete chloroplast genome of S. dalzielii was 144,580 bp in length. The genome is quadripartite in structure and consists of a large single-copy region (92,137 bp) and a small single-copy region (17,669 bp), which are separated by a pair of inverted repeats (each 17,387 bp). A total of 125 genes were annotated, including 80 protein-coding, 37 transfer RNA, and eight ribosomal RNA genes. The overall GC content was 36.4%. Phylogenetic analysis based on the complete chloroplast genome sequence of 21 taxa within the tribe Ruellieae of Acanthaceae using the maximum likelihood and Bayesian inference methods revealed that Strobilanthes diverged after Ruellia; S. dalzielii is closely related to S. tonkinensis. The genomic data obtained from this study will serve as valuable information to the species delimitation and genetic classification of Strobilanthes.
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Affiliation(s)
- Nuoguo Zeng
- Ganzhou Forestry Science Research Institute, Ganzhou, Jiangxi, China
| | - Weiping Gao
- Yongxin Forestry Bureau, Yongxin, Jiangxi, China
| | - Zhihui Chen
- School of Life Sciences, Guangdong Provincial Key Laboratory of Plant Resource, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Jing Yuan Chong
- Faculty of Health and Life Sciences, INTI International University, Nilai, Negeri Sembilan, Malaysia
| | - Shiou Yih Lee
- Faculty of Health and Life Sciences, INTI International University, Nilai, Negeri Sembilan, Malaysia
| | - Guoliang Xu
- Jiangxi Provincial Management Bureau for Jiulian Mountain National Natural Reserve, Longnan, Jiangxi, China
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22
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Fang Y, Wu D, Gao N, Lv M, Zhou M, Ma C, Sun Y, Cui B. Whole-genome sequencing and comparative genomic analyses of the medicinal fungus Sanguinoderma infundibulare in Ganodermataceae. G3 (Bethesda) 2024; 14:jkae005. [PMID: 38366555 PMCID: PMC10989896 DOI: 10.1093/g3journal/jkae005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 01/05/2024] [Indexed: 02/18/2024]
Abstract
Sanguinoderma infundibulare is a newly discovered species of Ganodermataceae known to have high medicinal and ecological values. In this study, the whole-genome sequencing and comparative genomic analyses were conducted to further understand Ganodermataceae's genomic structural and functional characteristics. Using the Illumina NovaSeq and PacBio Sequel platforms, 88 scaffolds were assembled to obtain a 48.99-Mb high-quality genome of S. infundibulare. A total of 14,146 protein-coding genes were annotated in the whole genome, with 98.6% of complete benchmarking universal single-copy orthologs (BUSCO) scores. Comparative genomic analyses were conducted among S. infundibulare, Sanguinoderma rugosum, Ganoderma lucidum, and Ganoderma sinense to determine their intergeneric differences. The 4 species were found to share 4,011 orthogroups, and 24 specific gene families were detected in the genus Sanguinoderma. The gene families associated with carbohydrate esterase in S. infundibulare were significantly abundant, which was reported to be involved in hemicellulose degradation. One specific gene family in Sanguinoderma was annotated with siroheme synthase, which may be related to the typical characteristics of fresh pore surface changing to blood red when bruised. This study enriched the available genome data for the genus Sanguinoderma, elucidated the differences between Ganoderma and Sanguinoderma, and provided insights into the characteristics of the genome structure and function of S. infundibulare.
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Affiliation(s)
- Yuxuan Fang
- State Key Laboratory of Efficient Production of Forest Resources, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
| | - Dongmei Wu
- Xinjiang Production and Construction Group Key Laboratory of Crop Germplasm Enhancement and Gene Resources Utilization, Biotechnology Research Institute, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi 832061, China
| | - Neng Gao
- Xinjiang Production and Construction Group Key Laboratory of Crop Germplasm Enhancement and Gene Resources Utilization, Biotechnology Research Institute, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi 832061, China
| | - Mengxue Lv
- State Key Laboratory of Efficient Production of Forest Resources, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
| | - Miao Zhou
- State Key Laboratory of Efficient Production of Forest Resources, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
| | - Chuangui Ma
- Beijing Jingcheng Biotechnology Co., Ltd, Beijing 100083, China
| | - Yifei Sun
- State Key Laboratory of Efficient Production of Forest Resources, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
| | - Baokai Cui
- State Key Laboratory of Efficient Production of Forest Resources, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
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23
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Wesseltoft JB, Danielsen CD, Andersen AM, de Jonge N, Olsen A, Rohde PD, Kristensen TN. Feeding Drosophila gut microbiomes from young and old flies modifies the microbiome. Sci Rep 2024; 14:7799. [PMID: 38565609 PMCID: PMC10987527 DOI: 10.1038/s41598-024-58500-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 03/30/2024] [Indexed: 04/04/2024] Open
Abstract
It is becoming increasingly evident that the myriad of microbes in the gut, within cells and attached to body parts (or roots of plants), play crucial roles for the host. Although this has been known for decades, recent developments in molecular biology allow for expanded insight into the abundance and function of these microbes. Here we used the vinegar fly, Drosophila melanogaster, to investigate fitness measures across the lifetime of flies fed a suspension of gut microbes harvested from young or old flies, respectively. Our hypothesis was that flies constitutively enriched with a 'Young microbiome' would live longer and be more agile at old age (i.e. have increased healthspan) compared to flies enriched with an 'Old microbiome'. Three major take home messages came out of our study: (1) the gut microbiomes of young and old flies differ markedly; (2) feeding flies with Young and Old microbiomes altered the microbiome of recipient flies and (3) the two different microbial diets did not have any effect on locomotor activity nor lifespan of the recipient flies, contradicting our working hypothesis. Combined, these results provide novel insight into the interplay between hosts and their microbiomes and clearly highlight that the phenotypic effects of gut transplants and probiotics can be complex and unpredictable.
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Affiliation(s)
| | | | | | - Nadieh de Jonge
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Anders Olsen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Palle Duun Rohde
- Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
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24
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Ando E, Taki K, Suzuki T, Kinoshita T. A novel semi-dominant mutation in brassinosteroid signaling kinase1 increases stomatal density. Front Plant Sci 2024; 15:1377352. [PMID: 38628368 PMCID: PMC11019013 DOI: 10.3389/fpls.2024.1377352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Accepted: 02/27/2024] [Indexed: 04/19/2024]
Abstract
Stomata play a pivotal role in balancing CO2 uptake for photosynthesis and water loss via transpiration. Thus, appropriate regulation of stomatal movement and its formation are crucial for plant growth and survival. Red and blue light induce phosphorylation of the C-terminal residue of the plasma membrane (PM) H+-ATPase, threonine, in guard cells, generating the driving force for stomatal opening. While significant progress has been made in understanding the regulatory mechanism of PM H+-ATPase in guard cells, the regulatory components for the phosphorylation of PM H+-ATPase have not been fully elucidated. Recently, we established a new immunohistochemical technique for detecting guard-cell PM H+-ATPase phosphorylation using leaves, which was expected to facilitate investigations with a single leaf. In this study, we applied the technique to genetic screening experiment to explore novel regulators for the phosphorylation of PM H+-ATPase in guard cells, as well as stomatal development. We successfully performed phenotyping using a single leaf. During the experiment, we identified a mutant exhibiting high stomatal density, jozetsu (jzt), named after a Japanese word meaning 'talkative'. We found that a novel semi-dominant mutation in BRASSINOSTEROID SIGNALING KINASE1 (BSK1) is responsible for the phenotype in jzt mutant. The present results demonstrate that the new immunohistochemical technique has a wide range of applications, and the novel mutation would provide genetic tool to expand our understanding of plant development mediated by brassinosteroid signaling.
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Affiliation(s)
- Eigo Ando
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Aichi, Japan
| | - Kyomi Taki
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya, Aichi, Japan
| | - Takamasa Suzuki
- Department of Biological Chemistry, College of Bioscience and Biotechnology, Chubu University, Kasugai, Aichi, Japan
| | - Toshinori Kinoshita
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Aichi, Japan
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya, Aichi, Japan
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25
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Talts T, Mosscrop LG, Williams D, Tregoning JS, Paulo W, Kohli A, Williams TC, Hoschler K, Ellis J, Lusignan SD, Zambon M. Robust and sensitive amplicon-based whole-genome sequencing assay of respiratory syncytial virus subtype A and B. Microbiol Spectr 2024; 12:e0306723. [PMID: 38411056 DOI: 10.1128/spectrum.03067-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 02/06/2024] [Indexed: 02/28/2024] Open
Abstract
Prevention of respiratory syncytial virus (RSV) infection is now a global health priority, with a long-acting monoclonal antibody and two RSV vaccines recently licenced for clinical use. Most licenced and candidate interventions target the RSV fusion (RSV-F) protein. New interventions may be associated with the spread of mutations, reducing susceptibility to antibody neutralization in RSV-F. There is a need for ongoing longitudinal global surveillance of circulating RSV strains. To achieve this large-scale genomic surveillance, a reliable, high-throughput RSV sequencing assay is required. Here we report an improved high-throughput RSV whole-genome sequencing (WGS) assay performed directly on clinical samples without additional enrichment, using a 4-primer-pool, short-amplicon PCR-tiling approach that is suitable for short-read sequencing platforms. Using upper respiratory tract (URT) RSV-positive clinical samples obtained from a sentinel network of primary care providers and from hospital patients (29.7% and 70.2%, respectively; n = 1,037), collected over the period 2019 to 2023, this assay had a threshold of approximately 4 × 103 to 8 × 103 copies/mL (RSV-B and RSV-A sub-types, respectively) as the lowest amount of virus needed in the sample to achieve >96% of whole-genome coverage at a high-quality level. Using a Ct value of 31 as an empirical cut-off, the overall assay success rate of obtaining >90% genome coverage at a read depth minimum of 20 was 96.83% for clinical specimens successfully sequenced from a total of 1,071. The RSV WGS approach described in this study has increased sensitivity compared to previous approaches and can be applied to clinical specimens without the requirement for enrichment. The updated approach produces sequences of high quality consistently and cost-effectively, suitable for implementation to underpin national programs for the surveillance of RSV genomic variation. IMPORTANCE In this paper, we report an improved high-throughput respiratory syncytial virus (RSV) whole-genome sequencing (WGS) assay performed directly on clinical samples, using a 4-primer-pool, short-amplicon PCR-tiling approach that is suitable for short-read sequencing platforms. The RSV WGS approach described in this study has increased sensitivity compared to previous approaches and can be applied to clinical specimens without the requirement for enrichment. The updated approach produces sequences of high quality consistently and cost-effectively, suitable for implementation to underpin national and global programs for the surveillance of RSV genomic variation. The quality of sequence produced is essential for preparedness for new interventions in monitoring antigenic escape, where a single point mutation might lead to a reduction in antibody binding effectiveness and neutralizing activity, or indeed in the monitoring of retaining susceptibility to neutralization by existing and new interventions.
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Affiliation(s)
- Tiina Talts
- UK Health Security Agency, London, United Kingdom
| | | | | | | | | | | | | | | | - Joanna Ellis
- UK Health Security Agency, London, United Kingdom
| | | | - Maria Zambon
- UK Health Security Agency, London, United Kingdom
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26
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Yang G, Anderson Williams S, He F, He Y, McIntyre K, Beckman AK, Nelson AC, Yohe SL. Immunohistochemistry screening for TP53 mutation in myeloid neoplasms in AZF-fixed bone marrow biopsies. Pathology 2024; 56:404-412. [PMID: 38341302 DOI: 10.1016/j.pathol.2023.11.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 10/18/2023] [Accepted: 11/01/2023] [Indexed: 02/12/2024]
Abstract
TP53 mutational status in myeloid neoplasms is prognostic and in acute myeloid leukaemia (AML) may lead to alternative induction therapy; therefore, rapid assessment is necessary for precision treatment. Assessment of multiple prognostic genes by next generation sequencing in AML is standard of care, but the turn-around time often cannot support rapid clinical decision making. Studies in haematological neoplasms suggest p53 immunohistochemistry (IHC) correlates with TP53 mutational status, but they have used variable criteria to define TP53 overexpression. p53 IHC was performed and interpreted on AZF-fixed, acid decalcified bone marrow biopsies on 47 cases of clonal myeloid neoplasms with TP53 mutations between 2016 and 2019 and 16 control samples. Results were scored by manual and digital analysis. Most TP53-mutated cases (81%) overexpressed p53 by digital analysis and manual analysis gave similar results. Among the nine TP53-mutated IHC-negative cases, seven (78%) were truncating mutations and two (22%) were single-hit missense mutations. Using a digital cut-off of at least 3% ≥1+ positive nuclei, the sensitivity and specificity are 81% and 100%; cases with loss-of-function mutations were more likely to be negative. In this cohort, p53 immunopositivity correlated with TP53 mutational status, especially missense mutations, with excellent specificity. Truncating TP53 mutations explain most IHC-negative cases, impacting the sensitivity. We demonstrate that p53 IHC can screen for TP53 mutations allowing quicker treatment decisions for most patients. However, not all patients will be identified, so molecular studies are required. Furthermore, cut-offs for positivity vary in the literature, consequently laboratories should independently validate their processes before adopting p53 IHC for clinical use. p53 IHC performs well to screen for TP53 mutations in AZF-fixed bone marrow. Performance in our setting differs from the literature, which shows variability of pre-analytic factors and cut-offs used to screen for TP53 mutations. Each laboratory should validate p53 IHC to screen for TP53 mutations in their unique setting.
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Affiliation(s)
- Guang Yang
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Sarah Anderson Williams
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Fiona He
- Division of Hematology, Oncology and Transplantation, Department of Medicine, University of Minnesota, MN, USA
| | - Yuyu He
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Kelsey McIntyre
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Amy K Beckman
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Andrew C Nelson
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Sophia L Yohe
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA.
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27
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He Q, Shi X, Yan J, Wu M, Gu C, Yu X. Circulating tumor DNA serial monitoring of relapse and responses to tislelizumab immunotherapy as second‑line monotherapy for metastatic esophageal squamous cell carcinoma: A prospective study. Mol Clin Oncol 2024; 20:29. [PMID: 38414510 PMCID: PMC10895470 DOI: 10.3892/mco.2024.2727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 01/08/2024] [Indexed: 02/29/2024] Open
Abstract
Anti-programmed cell death 1 immuno-monotherapy has become the second-line standard treatment for advanced esophageal squamous cell carcinoma (ESCC) after the failure of first-line chemotherapy. However, new biomarkers are still needed to identify patients at risk of tumor progression and to select patients with advanced ESCC who are likely to benefit from immunotherapy. A total of 12 patients with advanced ESCC treated with tislelizumab were prospectively enrolled and endoscopic biopsy samples were collected. Plasma was obtained prior to and after every 2-3 treatment cycles with tislelizumab and when disease progression occurred. Targeted sequencing of 425 genes from plasma cell-free DNA, DNA from leukocytes and fixed esophageal tumor biopsies was performed. The patients underwent imaging analyses every 6-8 weeks until disease progression. The association between status of circulating tumor DNA (ctDNA) or changes in ctDNA following tislelizumab immunotherapy and response, tumor progression and survival was determined. All patients had evaluable next-generation sequencing results at the time of analysis. The results showed that patients with ESCC with liver metastasis had a significantly shorter median progression-free survival (mPFS: 1.4 vs. 11.7 months; P=0.037). TSC complex subunit 2 [11.7 months vs. not reached (NR); P=0.004] and zinc finger protein 217 (11.7 months vs. NR; P=0.022) gene mutations were the independent and negative prognostic factors for median overall survival (OS), respectively. Of note, ctDNA dynamic changes expressed as ∆ mutant molecules per milliliter of plasma (∆MMPM; MMPM detected at the first monitoring time-point after the first infusion of tislelizumab as baseline MMPM) predicted progression-free survival (PFS) and OS more accurately compared to the ctDNA change of an individual gene. ∆MMPM <20% was an independent predictor of PFS (2.8 vs. 14.6 months; P=0.029), although there was no significant difference for OS (16.7 vs. 17.6 months; P=0.830). In conclusion, changes in ctDNA levels were associated with anti-tumor effects, progression and disease-specific survival. ctDNA sequencing is promising for predicting response and progression after tislelizumab immunotherapy as second-line monotherapy for advanced ESCC [the present study was part of the RATIONALE-302 study (ClinicalTrials.gov identifier no. NCT03430843; 29.01.2018)].
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Affiliation(s)
- Qiong He
- Department of Oncology, Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer, Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, P.R. China
| | - Xun Shi
- Department of Oncology, Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer, Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, P.R. China
| | - Junrong Yan
- Medical Department, Nanjing Geneseeq Technology Inc., Nanjing, Jiangsu 210032, P.R. China
| | - Mengmeng Wu
- Medical Department, Nanjing Geneseeq Technology Inc., Nanjing, Jiangsu 210032, P.R. China
| | - Cuiping Gu
- Department of Oncology, Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer, Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, P.R. China
| | - Xinmin Yu
- Department of Oncology, Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer, Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, P.R. China
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28
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Symmank D, Richter FC, Rendeiro AF. Navigating the thymic landscape through development: from cellular atlas to tissue cartography. Genes Immun 2024; 25:102-104. [PMID: 38341523 PMCID: PMC11023925 DOI: 10.1038/s41435-024-00257-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 01/22/2024] [Accepted: 01/26/2024] [Indexed: 02/12/2024]
Affiliation(s)
- Dörte Symmank
- Department of Dermatology, Medical University of Vienna, Vienna, 1090, Austria.
| | - Felix Clemens Richter
- Institute of Hygiene and Applied Immunology, Department of Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, 1090, Austria
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, 1090, Austria
| | - André F Rendeiro
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, 1090, Austria
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29
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Wu Y, Huang L, Li M, Cui X, Zhu J, Zhan Q, Wang C. Association between the lung microbiome and perioperative prognosis in lung transplant recipients. J Appl Microbiol 2024; 135:lxae089. [PMID: 38573839 DOI: 10.1093/jambio/lxae089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 02/29/2024] [Accepted: 04/03/2024] [Indexed: 04/06/2024]
Abstract
RATIONALE Studies have confirmed that the lung microbiome of lung transplant recipients is altered and serves as a prognostic indicator for long-term mortality. Other studies reported that the lung microbiome affects host immunity and the transcriptome. However, the lung microbiome composition at the early post-transplant period following lung transplantation is unclear, and the relationship of the lung microbiome with pulmonary immunity and the host transcriptome is also not well understood. OBJECTIVES We hypothesize that changes in the lung microbiome composition in the early post-transplant period may have a predictive value for perioperative outcomes following lung transplantation and that the lung microbiome is correlated with pulmonary immunity and the host transcriptome. Thus, this prospective study aimed at observing the lung microbiome composition in the early post-transplant period and the impact of the lung microbiome on pulmonary cytokines and the host transcriptome. Our findings will help us gain a comprehensive understanding of the distribution and significance of the lung microbiome in the early post-transplant period. METHODS An observational study was conducted to identify the lung microbiome and the host transcriptome characteristics using next-generation sequencing. Luminex was employed for quantifying alveolar cytokines. Spearman's correlation analysis was utilized to assess the impact of the lung microbiome on pulmonary immunity and differentially expressed genes in patients who died perioperatively after lung transplantation. RESULTS Patients with poor perioperative outcomes showed an increase in Mycoplasma and Arcobacter, a decrease of Gemella, and increased interleukin (IL)-10, IL-1β, and tumor necrosis factor (TNF)-α concentration. The lung microbiome correlates with lung immunity in lung transplant recipients. In the death group, the function of differentially expressed genes is associated with cell apoptosis, and promoting TNF production is upregulated. The lung microbiome is related to differentially expressed genes between the two groups. CONCLUSIONS The lung microbiome and cytokines can be considered as potential biomarkers for early prognosis in lung transplant recipients. The lung microbiome is associated with both lung immunity and differentially expressed genes in lung transplant recipients.
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Affiliation(s)
- Yuhan Wu
- Department of Respiratory and Critical Care Medicine, The Second Hospital of Harbin Medical University, Harbin 150086, China
- Harbin Medical University, Harbin 150086, China
| | - Linna Huang
- Department of Respiratory and Critical Care Medicine, China-Japan Friendship Hospital, Beijing 100029, China
| | - Min Li
- Department of Respiratory and Critical Care Medicine, China-Japan Friendship Hospital, Beijing 100029, China
| | - Xiaoyang Cui
- Department of Respiratory and Critical Care Medicine, China-Japan Friendship Hospital, Beijing 100029, China
| | - Jun Zhu
- Department of Respiratory and Critical Care Medicine, The Second Hospital of Harbin Medical University, Harbin 150086, China
- Harbin Medical University, Harbin 150086, China
| | - Qingyuan Zhan
- Department of Respiratory and Critical Care Medicine, China-Japan Friendship Hospital, Beijing 100029, China
| | - Chen Wang
- Department of Respiratory and Critical Care Medicine, The Second Hospital of Harbin Medical University, Harbin 150086, China
- Harbin Medical University, Harbin 150086, China
- Department of Respiratory and Critical Care Medicine, China-Japan Friendship Hospital, Beijing 100029, China
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30
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Sinim Kahraman N, Özgüç Çalışkan B, Kandemir N, Öner A, Dündar M, Özkul Y. ABCA4 variant screening in a Turkish cohort with Stargardt disease. Ophthalmic Genet 2024; 45:133-139. [PMID: 38369462 DOI: 10.1080/13816810.2024.2313490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 01/29/2024] [Indexed: 02/20/2024]
Abstract
PURPOSE This study aims to evaluate the ABCA4 variants in patients diagnosed with Stargardt disease. METHODS This is a retrospective study designed to investigate variants in the ABCA4 in Stargardt disease and the clinical findings of the cases. Sex, age, age of onset of symptoms, best-corrected visual acuity, color fundus photography, optical coherence tomography, and visual field test of the patients were recorded. Genetic analyses were screened, and patients with at least two variants in the ABCA4 were included in this study. RESULTS Twenty-seven patients diagnosed with Stargardt disease with the ABCA4 variants were included in this study. Twelve of them (44.4%) were female and fifteen (55.5%) were male. The mean age of the cases was 27.44 years (ranging from 8 to 56 years). Thirty different variants were detected in 54 ABCA4 alleles of 27 patients. The two most common pathogenic variants were c.5882 G>A p.(Gly1961Glu) and c.52C>T p.(Arg18Trp) in this cohort. Two novel variants were identified (c.3855_3856dup, c.1554 + 3_1554 + 4del) and the patient with the c.1554 + 3_1554 + 4del variant additionally had a different ABCA4 variant in trans. The other novel variant was homozygous. CONCLUSIONS In this study, two novel variants were described in a Turkish cohort with Stargardt disease. The variant c.52C>T p.(Arg18Trp) was the most common disease-causing variant besides the c.5882 G>A p.(Gly1961Glu) which was identified frequently in the previous studies. A larger sample size is necessary for describing different pathogenic variants and understanding the phenotype-genotype correlations.
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Affiliation(s)
| | - Büşra Özgüç Çalışkan
- Department of Medical Genetics, Erciyes University Medicine Faculty, Kayseri, Türkiye
| | - Nefise Kandemir
- Department of Medical Genetics, Kayseri Education and Research Hospital, Kayseri, Türkiye
| | - Ayşe Öner
- Department of Ophthalmology, Acibadem Hospital, İstanbul, Türkiye
| | - Munis Dündar
- Department of Medical Genetics, Erciyes University Medicine Faculty, Kayseri, Türkiye
| | - Yusuf Özkul
- Department of Medical Genetics, Erciyes University Medicine Faculty, Kayseri, Türkiye
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31
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Li J, Barnes S, Lefkowitz E, Yarar-Fisher C. Unveiling the connection between gut microbiome and metabolic health in individuals with chronic spinal cord injury. Physiol Genomics 2024; 56:317-326. [PMID: 38344780 DOI: 10.1152/physiolgenomics.00107.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 01/26/2024] [Accepted: 02/05/2024] [Indexed: 03/22/2024] Open
Abstract
Accumulating evidence has revealed that alterations in the gut microbiome following spinal cord injury (SCI) exhibit similarities to those observed in metabolic syndrome. Considering the causal role of gut dysbiosis in metabolic syndrome development, SCI-induced gut dysbiosis may be a previously unidentified contributor to the increased risk of cardiometabolic diseases, which has garnered attention. With a cross-sectional design, we evaluated the correlation between gut microbiome composition and functional potential with indicators of metabolic health among 46 individuals with chronic SCI. Gut microbiome communities were profiled using next-generation sequencing techniques. Indices of metabolic health, including fasting lipid profile, glucose tolerance, insulin resistance, and inflammatory markers, were assessed through fasting blood tests and an oral glucose tolerance test. We used multivariate statistical techniques (i.e., regularized canonical correlation analysis) to identify correlations between gut bacterial communities, functional pathways, and metabolic health indicators. Our findings spotlight bacterial species and functional pathways associated with complex carbohydrate degradation and maintenance of gut barrier integrity as potential contributors to improved metabolic health. Conversely, those correlated with detrimental microbial metabolites and gut inflammatory pathways demonstrated associations with poorer metabolic health outcomes. This cross-sectional investigation represents a pivotal initial step toward comprehending the intricate interplay between the gut microbiome and metabolic health in SCI. Furthermore, our results identified potential targets for future research endeavors to elucidate the role of the gut microbiome in metabolic syndrome in this population.NEW & NOTEWORTHY Spinal cord injury (SCI) is accompanied by gut dysbiosis and the impact of this on the development of metabolic syndrome in this population remains to be investigated. Our study used next-generation sequencing and multivariate statistical analyses to explore the correlations between gut microbiome composition, function, and metabolic health indices in individuals with chronic SCI. Our results point to potential gut microbial species and functional pathways that may be implicated in the development of metabolic syndrome.
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Affiliation(s)
- Jia Li
- Department of Physical Medicine and Rehabilitation, The Ohio State University, Columbus, Ohio, United States
| | - Stephen Barnes
- Department of Pharmacology and Toxicology, The University of Alabama at Birmingham, Birmingham, Alabama, United States
| | - Elliot Lefkowitz
- Department of Microbiology, The University of Alabama at Birmingham, Birmingham, Alabama, United States
| | - Ceren Yarar-Fisher
- Department of Physical Medicine and Rehabilitation, The Ohio State University, Columbus, Ohio, United States
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Awotoye W, Mossey PA, Hetmanski JB, Gowans LJ, Eshete MA, Adeyemo WL, Alade A, Zeng E, Adamson O, James O, Fashina A, Ogunlewe MO, Naicker T, Adeleke C, Busch T, Li M, Petrin A, Oladayo A, Kayali S, Olotu J, Sule V, Hassan M, Pape J, Aladenika ET, Donkor P, Arthur FK, Obiri-Yeboah S, Sabbah DK, Agbenorku P, Ray D, Plange-Rhule G, Oti AA, Albokhari D, Sobreira N, Dunnwald M, Beaty TH, Taub M, Marazita ML, Adeyemo AA, Murray JC, Butali A. Damaging Mutations in AFDN Contribute to Risk of Nonsyndromic Cleft Lip With or Without Cleft Palate. Cleft Palate Craniofac J 2024; 61:697-705. [PMID: 36384317 PMCID: PMC10185709 DOI: 10.1177/10556656221135926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Novel or rare damaging mutations have been implicated in the developmental pathogenesis of nonsyndromic cleft lip with or without cleft palate (nsCL ± P). Thus, we investigated the human genome for high-impact mutations that could explain the risk of nsCL ± P in our cohorts. We conducted next-generation sequencing (NGS) analysis of 130 nsCL ± P case-parent African trios to identify pathogenic variants that contribute to the risk of clefting. We replicated this analysis using whole-exome sequence data from a Brazilian nsCL ± P cohort. Computational analyses were then used to predict the mechanism by which these variants could result in increased risks for nsCL ± P. We discovered damaging mutations within the AFDN gene, a cell adhesion molecule (CAMs) that was previously shown to contribute to cleft palate in mice. These mutations include p.Met1164Ile, p.Thr453Asn, p.Pro1638Ala, p.Arg669Gln, p.Ala1717Val, and p.Arg1596His. We also discovered a novel splicing p.Leu1588Leu mutation in this protein. Computational analysis suggests that these amino acid changes affect the interactions with other cleft-associated genes including nectins (PVRL1, PVRL2, PVRL3, and PVRL4) CDH1, CTNNA1, and CTNND1. This is the first report on the contribution of AFDN to the risk for nsCL ± P in humans. AFDN encodes AFADIN, an important CAM that forms calcium-independent complexes with nectins 1 and 4 (encoded by the genes PVRL1 and PVRL4). This discovery shows the power of NGS analysis of multiethnic cleft samples in combination with a computational approach in the understanding of the pathogenesis of nsCL ± P.
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Affiliation(s)
- Waheed Awotoye
- Iowa Institute for Oral Health Research, University of Iowa, Iowa City, IA, USA
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA, USA
| | - Peter A. Mossey
- Department of Orthodontics, University of Dundee, Dundee, UK
| | - Jacqueline B. Hetmanski
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Lord J.J Gowans
- Department of Biochemistry and Biotechnology, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Mekonen A. Eshete
- Addis Ababa University, School Medicine, Surgical Department, Addis Ababa, Ethiopia
| | - Wasiu L. Adeyemo
- Department of Oral and Maxillofacial Surgery, University of Lagos, Lagos Nigeria
| | - Azeez Alade
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA, USA
- Department of Epidemiology, College of Public Health, University of Iowa, Iowa City, IA, USA
| | - Erliang Zeng
- Division of Biostatistics and Computational Biology, College of Dentistry, University of Iowa, Iowa City, IA, USA
| | - Olawale Adamson
- Department of Oral and Maxillofacial Surgery, University of Lagos, Lagos Nigeria
| | - Olutayo James
- Department of Oral and Maxillofacial Surgery, University of Lagos, Lagos Nigeria
| | - Azeez Fashina
- Department of Oral and Maxillofacial Surgery, University of Lagos, Lagos Nigeria
| | - Modupe O Ogunlewe
- Department of Oral and Maxillofacial Surgery, University of Lagos, Lagos Nigeria
| | - Thirona Naicker
- Department of Pediatrics, University of KwaZulu-Natal, South Africa
| | - Chinyere Adeleke
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA, USA
| | - Tamara Busch
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA, USA
| | - Mary Li
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA, USA
| | - Aline Petrin
- Iowa Institute for Oral Health Research, University of Iowa, Iowa City, IA, USA
| | - Abimbola Oladayo
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA, USA
| | - Sami Kayali
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA, USA
| | - Joy Olotu
- Department of Anatomy, University of Port Harcourt
| | - Veronica Sule
- Department of Operative Dentistry, College of Dentistry, University of Iowa, Iowa City, IA, USA
| | - Mohaned Hassan
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA, USA
| | - John Pape
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA, USA
| | - Emmanuel T. Aladenika
- Iowa Institute for Oral Health Research, University of Iowa, Iowa City, IA, USA
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA, USA
| | - Peter Donkor
- Department of Surgery, School of Medicine and Dentistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Fareed K.N. Arthur
- Department of Biochemistry and Biotechnology, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Solomon Obiri-Yeboah
- Department of Maxillofacial Sciences, School of Medicine and Dentistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Daniel K. Sabbah
- Department of Child Oral Health and Orthodontics, School of Medicine and Dentistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Pius Agbenorku
- Department of Surgery, School of Medicine and Dentistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Debashree Ray
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Gyikua Plange-Rhule
- Department of Child Health, School of Medicine and Dentistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Alexander Acheampong Oti
- Department of Maxillofacial Sciences, School of Medicine and Dentistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Daniah Albokhari
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University
| | - Nara Sobreira
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University
| | | | - Terri H. Beaty
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Margaret Taub
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Mary L. Marazita
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, School of Dental Medicine, and Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | | | | | - Azeez Butali
- Iowa Institute for Oral Health Research, University of Iowa, Iowa City, IA, USA
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA, USA
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Fukunaga N, Hayashi T, Yamada Y, Mizobuchi K, Ohta A, Nakano T. A novel stop-gain NF1 variant in neurofibromatosis type 1 and bilateral optic atrophy without optic gliomas. Ophthalmic Genet 2024; 45:186-192. [PMID: 37599594 DOI: 10.1080/13816810.2023.2245464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 06/25/2023] [Accepted: 08/01/2023] [Indexed: 08/22/2023]
Abstract
BACKGROUND Neurofibromatosis type 1 (NF1) is a multisystem disorder that primarily affects the skin and peripheral nervous system and is caused by chromosomal abnormalities and mostly truncating variants in the NF1 gene. Ocular complications such as Lisch nodules and optic pathway gliomas (OPGs) can occur in NF1 patients. Herein, we report a novel NF1 variant in an NF1 patient with bilateral optic atrophy. METHODS Ophthalmological examinations and genetic analyses were performed using targeted next-generation sequencing (NGS). RESULTS A 14-year-old girl diagnosed with NF1 visited our hospital with decreased visual acuity (VA). The patient had no family history of NF1 or visual impairment. Brain and orbital magnetic resonance imaging revealed no remarkable findings. Ophthalmoscopy revealed temporal pallor of the optic discs, which was confirmed by optical coherence tomography findings of significant thinning of the circumpapillary retinal nerve fiber layer in both eyes. At 23 years of age, the decimal-corrected VA had deteriorated to 0.2 in the right eye and 0.1 in the left eye. Additionally, the targeted NGS panel revealed a novel heterozygous stop-gain variant (p.Tyr628Ter) in the NF1 gene; however, no pathogenic variants in OPA1 or the mitochondrial DNA were identified. CONCLUSIONS A patient with NF1 without OPGs developed bilateral optic atrophy and carried a novel de novo stop-gain variant of NF1. Although the relationship between NF1 variants and bilateral optic atrophy remains unclear, further investigations are required.
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Affiliation(s)
- Naoko Fukunaga
- Department of Ophthalmology, Katsushika Medical Center, The Jikei University School of Medicine, Tokyo, Japan
| | - Takaaki Hayashi
- Department of Ophthalmology, Katsushika Medical Center, The Jikei University School of Medicine, Tokyo, Japan
- Department of Ophthalmology, The Jikei University School of Medicine, Tokyo, Japan
| | - Yuki Yamada
- Department of Ophthalmology, The Jikei University School of Medicine, Tokyo, Japan
| | - Kei Mizobuchi
- Department of Ophthalmology, The Jikei University School of Medicine, Tokyo, Japan
| | - Arihito Ohta
- Department of Dermatology, The Jikei University School of Medicine, Tokyo, Japan
| | - Tadashi Nakano
- Department of Ophthalmology, The Jikei University School of Medicine, Tokyo, Japan
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Kim MH, Kim SH, Lee G, Mok J, Lee MK, Song JS, Eom JS. Next-generation sequencing using tissue specimen collected with a 1.1 mm-diameter cryoprobe in patients with lung cancer. Respirology 2024; 29:333-339. [PMID: 38379178 DOI: 10.1111/resp.14680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 01/30/2024] [Indexed: 02/22/2024]
Abstract
BACKGROUND AND OBJECTIVE Next-generation sequencing (NGS) analysis is considered standard for lung cancer diagnosis in clinical practice. Little is known about the feasibility of NGS using tumour tissue sampled with a 1.1 mm-diameter cryoprobe. We aimed to investigate the suitability of specimens obtained by transbronchial cryobiopsy (TBC) using a 1.1 mm-diameter cryoprobe for NGS analysis. METHODS Patients with lung cancer who underwent TBC using a 1.1 mm-diameter cryoprobe for NGS testing between October 2020 and April 2023 were enrolled. A 4.0- or 3.0 mm-diameter bronchoscope with radial probe endobronchial ultrasound and virtual bronchoscopic navigation was used to detect peripheral lung lesions. All procedures were performed under fluoroscopic guidance. Data were analysed retrospectively. RESULTS A total of 56 patients underwent TBC using a 1.1 mm cryoprobe for NGS testing, during the study period. Most patients (98%) were in the advanced stage of lung cancer (recurrent or inoperable disease of stages III or IV). The diagnostic yield of NGS for DNA and RNA sequencing was 95% each (53 of 56). Moderate bleeding was noted in three patients (5%) and none of the study patients developed life-threatening complications, such as pneumothorax or lung infection. CONCLUSION TBC using a 1.1 mm-diameter cryoprobe is a useful and safe tool for NGS analysis, for both DNA and RNA sequencing.
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Affiliation(s)
- Mi-Hyun Kim
- Department of Internal Medicine, Pusan National University School of Medicine, Busan, Republic of Korea
- Department of Internal Medicine, Pusan National University Hospital, Busan, Republic of Korea
- Biomedical Research Institute, Pusan National University Hospital, Busan, Republic of Korea
| | - Soo Han Kim
- Department of Internal Medicine, Pusan National University School of Medicine, Busan, Republic of Korea
- Department of Internal Medicine, Pusan National University Hospital, Busan, Republic of Korea
| | - Geewon Lee
- Department of Radiology, Pusan National University School of Medicine, Busan, Republic of Korea
- Department of Radiology, Pusan National University Hospital, Busan, Republic of Korea
| | - Jeongha Mok
- Department of Internal Medicine, Pusan National University School of Medicine, Busan, Republic of Korea
- Department of Internal Medicine, Pusan National University Hospital, Busan, Republic of Korea
| | - Min Ki Lee
- Department of Internal Medicine, Pusan National University School of Medicine, Busan, Republic of Korea
- Department of Internal Medicine, Pusan National University Hospital, Busan, Republic of Korea
| | - Ju Sun Song
- GC Genome Corporation, Yongin, Republic of Korea
| | - Jung Seop Eom
- Department of Internal Medicine, Pusan National University School of Medicine, Busan, Republic of Korea
- Department of Internal Medicine, Pusan National University Hospital, Busan, Republic of Korea
- Biomedical Research Institute, Pusan National University Hospital, Busan, Republic of Korea
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Quail MA, Corton C, Uphill J, Keane J, Gu Y. Identifying the best PCR enzyme for library amplification in NGS. Microb Genom 2024; 10. [PMID: 38578268 DOI: 10.1099/mgen.0.001228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2024] Open
Abstract
Background. PCR amplification is a necessary step in many next-generation sequencing (NGS) library preparation methods [1, 2]. Whilst many PCR enzymes are developed to amplify single targets efficiently, accurately and with specificity, few are developed to meet the challenges imposed by NGS PCR, namely unbiased amplification of a wide range of different sizes and GC content. As a result PCR amplification during NGS library prep often results in bias toward GC neutral and smaller fragments. As NGS has matured, optimized NGS library prep kits and polymerase formulations have emerged and in this study we have tested a wide selection of available enzymes for both short-read Illumina library preparation and long fragment amplification ahead of long-read sequencing.We tested over 20 different hi-fidelity PCR enzymes/NGS amplification mixes on a range of Illumina library templates of varying GC content and composition, and find that both yield and genome coverage uniformity characteristics of the commercially available enzymes varied dramatically. Three enzymes Quantabio RepliQa Hifi Toughmix, Watchmaker Library Amplification Hot Start Master Mix (2X) 'Equinox' and Takara Ex Premier were found to give a consistent performance, over all genomes, that mirrored closely that observed for PCR-free datasets. We also test a range of enzymes for long-read sequencing by amplifying size fractionated S. cerevisiae DNA of average size 21.6 and 13.4 kb, respectively.The enzymes of choice for short-read (Illumina) library fragment amplification are Quantabio RepliQa Hifi Toughmix, Watchmaker Library Amplification Hot Start Master Mix (2X) 'Equinox' and Takara Ex Premier, with RepliQa also being the best performing enzyme from the enzymes tested for long fragment amplification prior to long-read sequencing.
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Affiliation(s)
| | - Craig Corton
- Wellcome Sanger Institute, Hinxton, Cambs., CB10 1SA, UK
| | - James Uphill
- Wellcome Sanger Institute, Hinxton, Cambs., CB10 1SA, UK
| | - Jacqueline Keane
- Department of Medicine, University of Cambridge, Cambridge, Cambs., CB2 1TN, UK
| | - Yong Gu
- Wellcome Sanger Institute, Hinxton, Cambs., CB10 1SA, UK
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Cordier AG, Zerbib E, Favier A, Dabi Y, Daraï E. Value of Non-Coding RNA Expression in Biofluids to Identify Patients at Low Risk of Pathologies Associated with Pregnancy. Diagnostics (Basel) 2024; 14:729. [PMID: 38611642 PMCID: PMC11011513 DOI: 10.3390/diagnostics14070729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Revised: 03/25/2024] [Accepted: 03/25/2024] [Indexed: 04/14/2024] Open
Abstract
Pregnancy-related complications (PRC) impact maternal and fetal morbidity and mortality and place a huge burden on healthcare systems. Thus, effective diagnostic screening strategies are crucial. Currently, national and international guidelines define patients at low risk of PRC exclusively based on their history, thus excluding the possibility of identifying patients with de novo risk (patients without a history of disease), which represents most women. In this setting, previous studies have underlined the potential contribution of non-coding RNAs (ncRNAs) to detect patients at risk of PRC. However, placenta biopsies or cord blood samples are required, which are not simple procedures. Our review explores the potential of ncRNAs in biofluids (fluids that are excreted, secreted, or developed because of a physiological or pathological process) as biomarkers for identifying patients with low-risk pregnancies. Beyond the regulatory roles of ncRNAs in placental development and vascular remodeling, we investigated their specific expressions in biofluids to determine favorable pregnancy outcomes as well as the most frequent pathologies of pregnant women. We report distinct ncRNA panels associated with PRC based on omics technologies and subsequently define patients at low risk. We present a comprehensive analysis of ncRNA expression in biofluids, including those using next-generation sequencing, shedding light on their predictive value in clinical practice. In conclusion, this paper underscores the emerging significance of ncRNAs in biofluids as promising biomarkers for risk stratification in PRC. The investigation of ncRNA expression patterns and their potential clinical applications is of diagnostic, prognostic, and theragnostic value and paves the way for innovative approaches to improve prenatal care and maternal and fetal outcomes.
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Affiliation(s)
| | - Elie Zerbib
- Department of Obstetrics and Reproductive Medicine, Sorbonne University, Hôpital Tenon, 4 Rue de la Chine, 75020 Paris, France; (A.-G.C.); (Y.D.)
| | | | | | - Emile Daraï
- Department of Obstetrics and Reproductive Medicine, Sorbonne University, Hôpital Tenon, 4 Rue de la Chine, 75020 Paris, France; (A.-G.C.); (Y.D.)
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Jaksik R, Szumała K, Dinh KN, Śmieja J. Multiomics-Based Feature Extraction and Selection for the Prediction of Lung Cancer Survival. Int J Mol Sci 2024; 25:3661. [PMID: 38612473 PMCID: PMC11011391 DOI: 10.3390/ijms25073661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 03/19/2024] [Accepted: 03/20/2024] [Indexed: 04/14/2024] Open
Abstract
Lung cancer is a global health challenge, hindered by delayed diagnosis and the disease's complex molecular landscape. Accurate patient survival prediction is critical, motivating the exploration of various -omics datasets using machine learning methods. Leveraging multi-omics data, this study seeks to enhance the accuracy of survival prediction by proposing new feature extraction techniques combined with unbiased feature selection. Two lung adenocarcinoma multi-omics datasets, originating from the TCGA and CPTAC-3 projects, were employed for this purpose, emphasizing gene expression, methylation, and mutations as the most relevant data sources that provide features for the survival prediction models. Additionally, gene set aggregation was shown to be the most effective feature extraction method for mutation and copy number variation data. Using the TCGA dataset, we identified 32 molecular features that allowed the construction of a 2-year survival prediction model with an AUC of 0.839. The selected features were additionally tested on an independent CPTAC-3 dataset, achieving an AUC of 0.815 in nested cross-validation, which confirmed the robustness of the identified features.
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Affiliation(s)
- Roman Jaksik
- Department of Systems Biology and Engineering, Silesian University of Technology, 44-100 Gliwice, Poland;
| | - Kamila Szumała
- Faculty of Automatic Control, Electronics and Computer Science, Silesian University of Technology, 44-100 Gliwice, Poland;
| | - Khanh Ngoc Dinh
- Irving Institute for Cancer Dynamics and Department of Statistics, Columbia University, New York, NY 10027, USA;
| | - Jarosław Śmieja
- Department of Systems Biology and Engineering, Silesian University of Technology, 44-100 Gliwice, Poland;
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Guo J, Lin LF, Oraskovich SV, Rivera de Jesús JA, Listgarten J, Schaffer DV. Computationally guided AAV engineering for enhanced gene delivery. Trends Biochem Sci 2024:S0968-0004(24)00054-9. [PMID: 38531696 DOI: 10.1016/j.tibs.2024.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 02/22/2024] [Accepted: 03/01/2024] [Indexed: 03/28/2024]
Abstract
Gene delivery vehicles based on adeno-associated viruses (AAVs) are enabling increasing success in human clinical trials, and they offer the promise of treating a broad spectrum of both genetic and non-genetic disorders. However, delivery efficiency and targeting must be improved to enable safe and effective therapies. In recent years, considerable effort has been invested in creating AAV variants with improved delivery, and computational approaches have been increasingly harnessed for AAV engineering. In this review, we discuss how computationally designed AAV libraries are enabling directed evolution. Specifically, we highlight approaches that harness sequences outputted by next-generation sequencing (NGS) coupled with machine learning (ML) to generate new functional AAV capsids and related regulatory elements, pushing the frontier of what vector engineering and gene therapy may achieve.
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Affiliation(s)
- Jingxuan Guo
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
| | - Li F Lin
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, USA
| | - Sydney V Oraskovich
- Department of Bioengineering, University of California, Berkeley, CA 94720, USA; Graduate Program in Bioengineering, University of California, San Francisco and University of California, Berkeley, CA 94720, USA
| | - Julio A Rivera de Jesús
- Department of Bioengineering, University of California, Berkeley, CA 94720, USA; Graduate Program in Bioengineering, University of California, San Francisco and University of California, Berkeley, CA 94720, USA; Department of Neurological Surgery, University of California, San Francisco, CA 94143, USA
| | - Jennifer Listgarten
- Department of Electrical Engineering and Computer Science, University of California, Berkeley, CA 94720, USA
| | - David V Schaffer
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA; Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, USA; Department of Bioengineering, University of California, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA.
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Grew E, Reddy M, Reichner H, Kim J, Salam M, Hashim A. Yield and Utility of Routine Epilepsy Panel Genetic Testing Among Young Patients With Seizures. J Child Neurol 2024:8830738241240516. [PMID: 38528770 DOI: 10.1177/08830738241240516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
Objective: We examined the yield of routine epilepsy panel genetic testing in pediatric patients. Methods: We retrospectively reviewed epilepsy genetic panel results routinely performed in the hospital or clinic on patients <8 years old from July 2021 to July 2023. We evaluated demographics, family history, seizure type, severity, and frequency, development, tone and movement abnormalities, dysmorphism, and electroencephalography (EEG) or magnetic resonance imaging (MRI) results as predictors of results. Results: 65 patients were included with mean age 4.5 years. Sixty percent of patients were male; 11 patients had pathogenic variants (16.9%), 7 were carriers for autosomal recessive conditions (10.8%), 36 had variants of uncertain significance (55.4%), and 11 tested negative (16.9%). Pathogenic variants and variants of uncertain significance were unassociated with demographics, clinical features, imaging, or family history. Conclusion: Variants identified have potential implications for treatment (SCN1), comorbidity screening (TSC1), reproduction (ATAD1, PSAT1, and CLN8), and prognostication (FOXG1). Patients not routinely screened for a genetic cause of epilepsy by our standard practices had clinically relevant results.
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Affiliation(s)
- Emily Grew
- Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Mayuri Reddy
- Rutgers New Jersey Medical School, Newark, NJ, USA
| | | | - Jinsoo Kim
- Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Misbah Salam
- Department of Pediatric Neurology, Children's Hospital of New Jersey at Newark Beth Israel Medical Center, Newark, NJ, USA
| | - Anjum Hashim
- Department of Pediatric Neurology, Children's Hospital of New Jersey at Newark Beth Israel Medical Center, Newark, NJ, USA
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40
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Kelly C, Raymond C, Han S, Lin Y, Chen L, Huang G, Dong J. DNA variants detected in primary and metastatic lung adenocarcinoma: a case report and review of the literature. Lab Med 2024:lmae019. [PMID: 38527227 DOI: 10.1093/labmed/lmae019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2024] Open
Abstract
Non-small cell lung cancer (NSCLC) has been found to have recurrent genetic abnormalities, and novel therapies targeting these aberrations have improved patient survival. In this study, specimens from benign tissue, primary tumors, and brain metastases were obtained at autopsy from a 55-year-old White female patient diagnosed with NSCLC and were examined using next-generation sequencing (NGS) and chromosomal microarray assay (CMA). No genetic aberrations were noted in the benign tissue; however, NGS identified a mutation in the KRAS proto-oncogene, GTPase (KRAS): KRAS exon 2 p.G12D in primary and metastatic tumor specimens. We observed 7 DNA copy number aberrations (CNAs) in primary and metastatic tumor specimens; an additional 7 CNAs were exclusively detected in the metastatic tumor specimens. These DNA alterations may be genetic drivers in the pathogenesis of the tumor specimen from our patient and may serve as biomarkers for the classification and prognosis of NSCLC.
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Affiliation(s)
- Christina Kelly
- John Sealy School of Medicine, University of Texas Medical Branch, Galveston, TX
| | - Caitlin Raymond
- Department of Pathology, University of Texas Medical Branch, Galveston, TX
| | - Song Han
- Department of Pathology, University of Texas Medical Branch, Galveston, TX
| | - Youmin Lin
- Department of Pathology, University of Texas Medical Branch, Galveston, TX
| | - Linyijia Chen
- Department of Pathology, University of Texas Medical Branch, Galveston, TX
| | - Gengming Huang
- Department of Pathology, University of Texas Medical Branch, Galveston, TX
| | - Jianli Dong
- Department of Pathology, University of Texas Medical Branch, Galveston, TX
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Petiti J, Pignochino Y, Schiavon A, Giugliano E, Berrino E, Giordano G, Itri F, Dragani M, Cilloni D, Lo Iacono M. Comprehensive Molecular Profiling of NPM1-Mutated Acute Myeloid Leukemia Using RNAseq Approach. Int J Mol Sci 2024; 25:3631. [PMID: 38612443 PMCID: PMC11011776 DOI: 10.3390/ijms25073631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 03/18/2024] [Accepted: 03/22/2024] [Indexed: 04/14/2024] Open
Abstract
Acute myeloid leukemia (AML) is a complex hematologic malignancy with high morbidity and mortality. Nucleophosmin 1 (NPM1) mutations occur in approximately 30% of AML cases, and NPM1-mutated AML is classified as a distinct entity. NPM1-mutated AML patients without additional genetic abnormalities have a favorable prognosis. Despite this, 30-50% of them experience relapse. This study aimed to investigate the potential of total RNAseq in improving the characterization of NPM1-mutated AML patients. We explored genetic variations independently of myeloid stratification, revealing a complex molecular scenario. We showed that total RNAseq enables the uncovering of different genetic alterations and clonal subtypes, allowing for a comprehensive evaluation of the real expression of exome transcripts in leukemic clones and the identification of aberrant fusion transcripts. This characterization may enhance understanding and guide improved treatment strategies for NPM1mut AML patients, contributing to better outcomes. Our findings underscore the complexity of NPM1-mutated AML, supporting the incorporation of advanced technologies for precise risk stratification and personalized therapeutic strategies. The study provides a foundation for future investigations into the clinical implications of identified genetic variations and highlights the importance of evolving diagnostic approaches in leukemia management.
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Affiliation(s)
- Jessica Petiti
- Division of Advanced Materials Metrology and Life Sciences, Istituto Nazionale di Ricerca Metrologica (INRiM), 10135 Turin, Italy;
| | - Ymera Pignochino
- Department of Clinical and Biological Sciences, University of Turin, 10043 Orbassano, Italy; (Y.P.); (A.S.); (F.I.); (D.C.)
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy; (E.B.); (G.G.)
| | - Aurora Schiavon
- Department of Clinical and Biological Sciences, University of Turin, 10043 Orbassano, Italy; (Y.P.); (A.S.); (F.I.); (D.C.)
| | - Emilia Giugliano
- Clinical and Microbiological Analysis Laboratory, San Luigi Gonzaga Hospital, 10043 Orbassano, Italy;
| | - Enrico Berrino
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy; (E.B.); (G.G.)
- Department of Medical Sciences, University of Turin, 10126 Turin, Italy
| | - Giorgia Giordano
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy; (E.B.); (G.G.)
- Department of Oncology, University of Turin, 10043 Orbassano, Italy
| | - Federico Itri
- Department of Clinical and Biological Sciences, University of Turin, 10043 Orbassano, Italy; (Y.P.); (A.S.); (F.I.); (D.C.)
| | - Matteo Dragani
- Division of Hematology and Cellular Therapies, San Martino Hospital, IRCCS, 16132 Genova, Italy;
| | - Daniela Cilloni
- Department of Clinical and Biological Sciences, University of Turin, 10043 Orbassano, Italy; (Y.P.); (A.S.); (F.I.); (D.C.)
| | - Marco Lo Iacono
- Department of Clinical and Biological Sciences, University of Turin, 10043 Orbassano, Italy; (Y.P.); (A.S.); (F.I.); (D.C.)
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Viggiano M, Ceroni F, Visconti P, Posar A, Scaduto MC, Sandoni L, Baravelli I, Cameli C, Rochat MJ, Maresca A, Vaisfeld A, Gentilini D, Calzari L, Carelli V, Zody MC, Maestrini E, Bacchelli E. Genomic analysis of 116 autism families strengthens known risk genes and highlights promising candidates. NPJ Genom Med 2024; 9:21. [PMID: 38519481 PMCID: PMC10959942 DOI: 10.1038/s41525-024-00411-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 02/27/2024] [Indexed: 03/25/2024] Open
Abstract
Autism spectrum disorder (ASD) is a complex neurodevelopmental condition with a strong genetic component in which rare variants contribute significantly to risk. We performed whole genome and/or exome sequencing (WGS and WES) and SNP-array analysis to identify both rare sequence and copy number variants (SNVs and CNVs) in 435 individuals from 116 ASD families. We identified 37 rare potentially damaging de novo SNVs (pdSNVs) in the cases (n = 144). Interestingly, two of them (one stop-gain and one missense variant) occurred in the same gene, BRSK2. Moreover, the identification of 8 severe de novo pdSNVs in genes not previously implicated in ASD (AGPAT3, IRX5, MGAT5B, RAB8B, RAP1A, RASAL2, SLC9A1, YME1L1) highlighted promising candidates. Potentially damaging CNVs (pdCNVs) provided support to the involvement of inherited variants in PHF3, NEGR1, TIAM1 and HOMER1 in neurodevelopmental disorders (NDD), although mostly acting as susceptibility factors with incomplete penetrance. Interpretation of identified pdSNVs/pdCNVs according to the ACMG guidelines led to a molecular diagnosis in 19/144 cases, although this figure represents a lower limit and is expected to increase thanks to further clarification of the role of likely pathogenic variants in ASD/NDD candidate genes not yet established. In conclusion, our study highlights promising ASD candidate genes and contributes to characterize the allelic diversity, mode of inheritance and phenotypic impact of de novo and inherited risk variants in ASD/NDD genes.
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Affiliation(s)
- Marta Viggiano
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Fabiola Ceroni
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
- Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, UK
| | - Paola Visconti
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOSI Disturbi dello Spettro Autistico, Bologna, Italy
| | - Annio Posar
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOSI Disturbi dello Spettro Autistico, Bologna, Italy
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Maria Cristina Scaduto
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOSI Disturbi dello Spettro Autistico, Bologna, Italy
| | - Laura Sandoni
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Irene Baravelli
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Cinzia Cameli
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Magali J Rochat
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Functional and Molecular Neuroimaging Unit, Bologna, Italy
| | - Alessandra Maresca
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna, Italy
| | - Alessandro Vaisfeld
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Davide Gentilini
- Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy
- Bioinformatics and Statistical Genomic Unit, IRCCS Istituto Auxologico Italiano, Milan, Italy
| | - Luciano Calzari
- Bioinformatics and Statistical Genomic Unit, IRCCS Istituto Auxologico Italiano, Milan, Italy
| | - Valerio Carelli
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna, Italy
| | | | - Elena Maestrini
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy.
| | - Elena Bacchelli
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy.
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Azizi H, Bonyadi M, Rafat A. A novel splice site variant of the BBS2 gene in a patient with Bardet-Biedl syndrome. Hum Genome Var 2024; 11:12. [PMID: 38514630 PMCID: PMC10957965 DOI: 10.1038/s41439-024-00269-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 02/01/2024] [Accepted: 02/14/2024] [Indexed: 03/23/2024] Open
Affiliation(s)
- Hasan Azizi
- Animal Biology Department, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | - Mortaza Bonyadi
- Center of Excellence for Biodiversity, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran.
| | - Abbas Rafat
- Department of Animal Science, University of Tabriz, Tabriz, Iran
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Yay E, Yilmaz M, Toygar H, Balci N, Alvarez Rivas C, Bolluk Kılıç B, Zirh A, Paster BJ, Kantarci A. Oral and gut microbial profiling in periodontitis and Parkinson's disease. J Oral Microbiol 2024; 16:2331264. [PMID: 38528960 PMCID: PMC10962298 DOI: 10.1080/20002297.2024.2331264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 03/11/2024] [Indexed: 03/27/2024] Open
Abstract
Objectives We tested the hypothesis that Parkinson's disease (PA) alters the periodontitis-associated oral microbiome. Method Patients with periodontitis with Parkinson's disease (PA+P) and without PA (P) and systemically and periodontally healthy individuals (HC) were enrolled. Clinical, periodontal and neurological parameters were recorded. The severity of PA motor functions was measured. Unstimulated saliva samples and stool samples were collected. Next-generation sequencing of 16S ribosomal RNA (V1-V3 regions) was performed. Results PA patients had mild-to-moderate motor dysfunction and comparable plaque scores as those without, indicating that oral hygiene was efficient in the PA+P group. In saliva, there were statistically significant differences in beta diversity between HC and PA+P (p = 0.001), HC and P (p = 0.001), and P and PA+P (p = 0.028). The microbial profiles of saliva and fecal samples were distinct. Mycoplasma faucium, Tannerella forsythia, Parvimonas micra, and Saccharibacteria (TM7) were increased in P; Prevotella pallens, Prevotella melaninogenica, Neisseria multispecies were more abundant in PA+P group, Ruthenibacterium lactatiformans, Dialister succinatiphilus, Butyrivibrio crossotus and Alloprevotella tannerae were detected in fecal samples in P groups compared to healthy controls. Conclusions No significant differences were detected between Parkinson's and non-Parkinson's gut microbiomes, suggesting that Parkinson's disease modifies the oral microbiome in periodontitis subjects independent of the gut microbiome.
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Affiliation(s)
- Ekin Yay
- Department of Applied Oral Sciences, The ADA Forsyth Institute, Cambridge, MA, USA
- Periodontist, Private Practice, Istanbul, Turkey
| | - Melis Yilmaz
- Department of Applied Oral Sciences, The ADA Forsyth Institute, Cambridge, MA, USA
- Department of Periodontology, Istanbul Medipol University, Istanbul, Turkey
| | - Hilal Toygar
- Department of Periodontology, Istanbul Medipol University, Istanbul, Turkey
| | - Nur Balci
- Department of Periodontology, Istanbul Medipol University, Istanbul, Turkey
| | - Carla Alvarez Rivas
- Department of Applied Oral Sciences, The ADA Forsyth Institute, Cambridge, MA, USA
- Department of Oral Microbiology and Infection, Harvard School of Dental Medicine, Boston, MA, USA
| | | | - Ali Zirh
- Department of Neurology, Istanbul Medipol University, Istanbul, Turkey
| | - Bruce J. Paster
- Department of Applied Oral Sciences, The ADA Forsyth Institute, Cambridge, MA, USA
- Department of Oral Microbiology and Infection, Harvard School of Dental Medicine, Boston, MA, USA
| | - Alpdogan Kantarci
- Department of Applied Oral Sciences, The ADA Forsyth Institute, Cambridge, MA, USA
- Department of Oral Microbiology and Infection, Harvard School of Dental Medicine, Boston, MA, USA
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Lee H, Shin K, Lee Y, Lee S, Lee S, Lee E, Kim SW, Shin HY, Kim JH, Chung J, Kwon S. Identification of B cell subsets based on antigen receptor sequences using deep learning. Front Immunol 2024; 15:1342285. [PMID: 38576618 PMCID: PMC10991714 DOI: 10.3389/fimmu.2024.1342285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 03/07/2024] [Indexed: 04/06/2024] Open
Abstract
B cell receptors (BCRs) denote antigen specificity, while corresponding cell subsets indicate B cell functionality. Since each B cell uniquely encodes this combination, physical isolation and subsequent processing of individual B cells become indispensable to identify both attributes. However, this approach accompanies high costs and inevitable information loss, hindering high-throughput investigation of B cell populations. Here, we present BCR-SORT, a deep learning model that predicts cell subsets from their corresponding BCR sequences by leveraging B cell activation and maturation signatures encoded within BCR sequences. Subsequently, BCR-SORT is demonstrated to improve reconstruction of BCR phylogenetic trees, and reproduce results consistent with those verified using physical isolation-based methods or prior knowledge. Notably, when applied to BCR sequences from COVID-19 vaccine recipients, it revealed inter-individual heterogeneity of evolutionary trajectories towards Omicron-binding memory B cells. Overall, BCR-SORT offers great potential to improve our understanding of B cell responses.
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Affiliation(s)
- Hyunho Lee
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, Republic of Korea
| | - Kyoungseob Shin
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, Republic of Korea
| | - Yongju Lee
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, Republic of Korea
| | - Soobin Lee
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, Republic of Korea
| | - Seungyoun Lee
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Biomedical Science, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Eunjae Lee
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Biomedical Science, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Seung Woo Kim
- Department of Neurology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Ha Young Shin
- Department of Neurology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jong Hoon Kim
- Department of Dermatology and Cutaneous Biology Research Institute, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Junho Chung
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Biomedical Science, Seoul National University College of Medicine, Seoul, Republic of Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Sunghoon Kwon
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, Republic of Korea
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, Republic of Korea
- Bio-MAX Institute, Seoul National University, Seoul, Republic of Korea
- Inter-University Semiconductor Research Center, Seoul National University, Seoul, Republic of Korea
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46
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Lou E, Xiu J, Baca Y, Saeed A, Prakash A, Gholami S, Subramanian S, Starr TK, Fontana E, Pandey R, Lenz HJ, Shields AF, Nabhan C, Oberley M, Seeber A, El-Deiry W. Differential landscape of immune evasion in oncogenic RAS-driven primary and metastatic colorectal cancers. Mol Ther Oncol 2024; 32:200786. [PMID: 38596288 PMCID: PMC10963927 DOI: 10.1016/j.omton.2024.200786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 02/26/2024] [Accepted: 02/26/2024] [Indexed: 04/11/2024]
Abstract
Oncogenic drivers such as KRAS extensively modulate the tumor inflammatory microenvironment (TIME) of colorectal cancer (CRC). The influence of KRAS on modulating immune cell composition remains unclear. The objective of this study was to identify signatures of infiltrative immune cells and distinctive patterns that differ between RAS wild-type (WT) and oncogenic mutant (MT) CRC that explain immune evasion in MT tumors. A total of 7,801 CRC specimens were analyzed using next-generation DNA sequencing, whole-exome sequencing, and/or whole transcriptome sequencing. Deficiency of mismatch repair (dMMR)/microsatellite instability (MSI) and tumor mutation burden (TMB) were also assessed. KRAS mutations were present in 48% of CRC, similarly distributed in patients younger than vs. 50 years and older. In microsatellite stable (MSS) KRAS MT tumors, composition of the TIME included higher neutrophil infiltration and lower infiltration of B cells. MSI-H/dMMR was significantly more prevalent in RAS WT (9.1%) than in KRAS MT (2.9%) CRC. In MSS CRC, TMB-high cases were significantly higher in RAS MT (3.1%) than in RAS WT (2.1%) tumors. KRAS and NRAS mutations are associated with increased neutrophil infiltration, with codon-specific differences. These results demonstrate significant differences in the TIME of RAS mutant CRC that match previous reports of immunoevasive characteristics of such tumors.
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Affiliation(s)
- Emil Lou
- Division of Hematology, Oncology, and Transplantation, Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | | | | | - Anwaar Saeed
- University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Ajay Prakash
- Division of Hematology, Oncology, and Transplantation, Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | | | | | - Timothy K. Starr
- Department of Obstetrics and Gynecology, Division of Gynecologic Oncology, University of Minnesota, Minneapolis, MN, USA
| | - Elisa Fontana
- Drug Development Unit, Sarah Cannon Research Institute UK, Marylebone, London, UK
| | - Ritu Pandey
- Arizona Cancer Center, Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ, USA
| | - Heinz-Josef Lenz
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Anthony F. Shields
- Department of Oncology, Karmanos Cancer Institute, Wayne State University, Detroit, MI, USA
| | | | | | - Andreas Seeber
- Department of Internal Medicine V (Hematology and Oncology), Comprehensive Cancer Center Innsbruck, Medical University of Innsbruck, Innsbruck, Austria
| | - Wafik El-Deiry
- Laboratory of Translational Oncology and Experimental Cancer Therapeutics, Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Legorreta Cancer Center, Brown University, Providence, RI, USA
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Guaschino M, Garello M, Nari L, Zhimo YV, Droby S, Spadaro D. Soil, rhizosphere, and root microbiome in kiwifruit vine decline, an emerging multifactorial disease. Front Microbiol 2024; 15:1330865. [PMID: 38577679 PMCID: PMC10991698 DOI: 10.3389/fmicb.2024.1330865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 02/14/2024] [Indexed: 04/06/2024] Open
Abstract
Kiwifruit vine decline syndrome (KVDS) is characterized by severe root system impairment, which leads to irreversible wilting of the canopy. Plants usually collapse rapidly from the appearance of the first aboveground symptoms, without recovery even in the following seasons. The syndrome has been negatively impacting kiwifruit yield in different areas of Italy, the main producing European country, since its first outbreak in 2012. To date, a unique, common causal factor has yet to be found, and the syndrome is referred to as multifactorial. In this article, we investigated the whole biotic community (fungi, bacteria, and oomycetes) associated with the development of KVDS in three different belowground matrices/compartments (soil, rhizosphere, and root). Sampling was performed at both healthy and affected sites located in the main kiwifruit-producing area of Northwestern Italy. To address the multifactorial nature of the syndrome and to investigate the potential roles of abiotic factors in shaping these communities, a physicochemical analysis of soils was also performed. This study investigates the associations among taxonomic groups composing the microbiome and also between biotic and abiotic factors. Dysbiosis was considered as a driving event in shaping KVDS microbial communities. The results obtained from this study highlight the role of the oomycete genus Phytopythium, which resulted predominantly in the oomycete community composition of diseased matrices, though it was also present in healthy ones. Both bacterial and fungal communities resulted in a high richness of genera and were highly correlated to the sampling site and matrix, underlining the importance of multiple location sampling both geographically and spatially. The rhizosphere community associated with KVDS was driven by a dysbiotic process. In addition, analysis of the association network in the diseased rhizosphere revealed the presence of potential cross-kingdom competition for plant-derived carbon between saprobes, oomycetes, and bacteria.
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Affiliation(s)
- Micol Guaschino
- Department of Agricultural, Forestry and Food Sciences (DiSAFA), University of Torino, Grugliasco, Italy
- Interdepartmental Centre for Innovation in Agro-environmental Sector – AGROINNOVA, University of Turin, Grugliasco, Italy
| | - Marco Garello
- Department of Agricultural, Forestry and Food Sciences (DiSAFA), University of Torino, Grugliasco, Italy
- Interdepartmental Centre for Innovation in Agro-environmental Sector – AGROINNOVA, University of Turin, Grugliasco, Italy
| | | | - Yeka V. Zhimo
- Department of Postharvest Science, ARO, The Volcani Center, Rishon LeZion, Israel
| | - Samir Droby
- Department of Postharvest Science, ARO, The Volcani Center, Rishon LeZion, Israel
| | - Davide Spadaro
- Department of Agricultural, Forestry and Food Sciences (DiSAFA), University of Torino, Grugliasco, Italy
- Interdepartmental Centre for Innovation in Agro-environmental Sector – AGROINNOVA, University of Turin, Grugliasco, Italy
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Zeeb M, Frischknecht P, Huber M, Schenkel CD, Neumann K, Leeman C, Notter J, Rauch A, Stöckle M, Cavassini M, Bernasconi E, Braun DL, Günthard HF, Metzner KJ, Kouyos RD. Genetic diversity from proviral DNA as a proxy for time since HIV-1 infection. J Infect Dis 2024:jiae149. [PMID: 38507572 DOI: 10.1093/infdis/jiae149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 03/11/2024] [Accepted: 03/18/2024] [Indexed: 03/22/2024] Open
Abstract
HIV-1 RNA genetic diversity predicts time since infection which is important for clinical care and research. It's unclear, however, whether proviral DNA genetic diversity sampled under suppressive antiretroviral therapy can be used for this purpose. We tested whether proviral genetic diversity from NGS sequences predicts time since infection and recency in 221 people with HIV-1 with known infection time. Proviral diversity was significantly associated with time since infection (p<5*10-07, R2 up to 25%) and predictive of treatment initiation during recent infection (AUC-ROC up to 0.85). This shows the utility of proviral genetic diversity as a proxy for time since infection.
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Affiliation(s)
- Marius Zeeb
- Department. of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland
- Institute of Medical Virology, University Zurich, 8057 Zurich, Switzerland
| | - Paul Frischknecht
- Department. of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Michael Huber
- Institute of Medical Virology, University Zurich, 8057 Zurich, Switzerland
| | - Corinne D Schenkel
- Department. of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Kathrin Neumann
- Department. of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Christine Leeman
- Department. of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Julia Notter
- Division of Infectious Diseases and Hospital Epidemiology, Cantonal Hospital St Gallen, 9007 St. Gallen, Switzerland
| | - Andri Rauch
- Department of Infectious Diseases, Inselspital, Bern University Hospital, University of Bern, 3010 Bern, Switzerland
| | - Marcel Stöckle
- Division of Infectious Diseases & Hospital Epidemiology, University Hospital Basel, 4031 Basel, Switzerland
- Medical Faculty, University of Basel, 4031 Basel, Switzerland
| | - Matthias Cavassini
- Division of Infectious Diseases, University Hospital Lausanne, University of Lausanne, 1011 Lausanne, Switzerland
| | - Enos Bernasconi
- Division of infectious diseases, Ente Ospedaliero Cantonale, Lugano, University of Geneva and University of Southern Switzerland, 6900 Lugano, Switzerland
| | - Dominique L Braun
- Department. of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Huldrych F Günthard
- Department. of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland
- Institute of Medical Virology, University Zurich, 8057 Zurich, Switzerland
| | - Karin J Metzner
- Department. of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland
- Institute of Medical Virology, University Zurich, 8057 Zurich, Switzerland
| | - Roger D Kouyos
- Department. of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland
- Institute of Medical Virology, University Zurich, 8057 Zurich, Switzerland
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49
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Fu Y, Chen YS, Xia DY, Luo XD, Luo HT, Pan J, Ma WQ, Li JZ, Mo QY, Tu Q, Li MM, Zhao Y, Li Y, Huang YT, Chen ZX, Li ZJ, Bernard L, Dione M, Zhang YM, Miao K, Chen JY, Zhu SS, Ren J, Zhou LJ, Jiang XZ, Chen J, Lin ZP, Chen JP, Ye H, Cao QY, Zhu YW, Yang L, Wang X, Wang WC. Lactobacillus rhamnosus GG ameliorates hyperuricemia in a novel model. NPJ Biofilms Microbiomes 2024; 10:25. [PMID: 38509085 PMCID: PMC10954633 DOI: 10.1038/s41522-024-00486-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 02/06/2024] [Indexed: 03/22/2024] Open
Abstract
Hyperuricemia (HUA) is a metabolic syndrome caused by abnormal purine metabolism. Although recent studies have noted a relationship between the gut microbiota and gout, whether the microbiota could ameliorate HUA-associated systemic purine metabolism remains unclear. In this study, we constructed a novel model of HUA in geese and investigated the mechanism by which Lactobacillus rhamnosus GG (LGG) could have beneficial effects on HUA. The administration of antibiotics and fecal microbiota transplantation (FMT) experiments were used in this HUA goose model. The effects of LGG and its metabolites on HUA were evaluated in vivo and in vitro. Heterogeneous expression and gene knockout of LGG revealed the mechanism of LGG. Multi-omics analysis revealed that the Lactobacillus genus is associated with changes in purine metabolism in HUA. This study showed that LGG and its metabolites could alleviate HUA through the gut-liver-kidney axis. Whole-genome analysis, heterogeneous expression, and gene knockout of LGG enzymes ABC-type multidrug transport system (ABCT), inosine-uridine nucleoside N-ribohydrolase (iunH), and xanthine permease (pbuX) demonstrated the function of nucleoside degradation in LGG. Multi-omics and a correlation analysis in HUA patients and this goose model revealed that a serum proline deficiency, as well as changes in Collinsella and Lactobacillus, may be associated with the occurrence of HUA. Our findings demonstrated the potential of a goose model of diet-induced HUA, and LGG and proline could be promising therapies for HUA.
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Affiliation(s)
- Yang Fu
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Yong-Song Chen
- Clinical Research Center, The First Affiliated Hospital of Shantou University Medical College, Shantou, 515041, China
| | - Dai-Yang Xia
- School of Marine Sciences, Sun Yat-sen University, and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519082, China
| | - Xiao-Dan Luo
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Hao-Tong Luo
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Jie Pan
- Hunan Shihua Biotech Co. Ltd., Changsha, 410000, China
| | - Wei-Qing Ma
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Jin-Ze Li
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Qian-Yuan Mo
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Qiang Tu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, Shandong, China
| | - Meng-Meng Li
- School of Agricultural Science and Engineering, Liaocheng University, Liaocheng, 252000, China
| | - Yue Zhao
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Yu Li
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Yi-Teng Huang
- Clinical Research Center, The First Affiliated Hospital of Shantou University Medical College, Shantou, 515041, China
| | - Zhi-Xian Chen
- Clinical Research Center, The First Affiliated Hospital of Shantou University Medical College, Shantou, 515041, China
| | - Zhen-Jun Li
- Key Laboratory of Carcinogenesis and Translational Research, Departments of Lymphoma, Radiology and Nuclear Medicine, Peking University Cancer Hospital and Institute, Beijing, 100080, China
| | - Lukuyu Bernard
- International Livestock Research Institute, Nairobi, 00100, Kenya
| | - Michel Dione
- International Livestock Research Institute, Nairobi, 00100, Kenya
| | - You-Ming Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, Shandong, China
| | - Kai Miao
- Cancer Center, Faculty of Health Sciences, University of Macau, Macau, SAR, China
| | - Jian-Ying Chen
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Shan-Shan Zhu
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Jie Ren
- Department of Rheumatology and Immunology, The First Affiliated Hospital of Jinan University, Guangzhou, 510630, China
| | - Ling-Juan Zhou
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Xian-Zhi Jiang
- Microbiome Research Center, Moon (Guangzhou) Biotech Co. Ltd., Guangzhou, 510535, China
| | - Juan Chen
- Microbiome Research Center, Moon (Guangzhou) Biotech Co. Ltd., Guangzhou, 510535, China
| | - Zhen-Ping Lin
- Shantou Baisha Research Institute of Origin Species of Poultry and Stock, Shantou, 515041, China
| | - Jun-Peng Chen
- Shantou Baisha Research Institute of Origin Species of Poultry and Stock, Shantou, 515041, China
| | - Hui Ye
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Qing-Yun Cao
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Yong-Wen Zhu
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Lin Yang
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China.
| | - Xue Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, Shandong, China.
| | - Wen-Ce Wang
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China.
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50
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Gunter HM, Youlten SE, Reis ALM, McCubbin T, Madala BS, Wong T, Stevanovski I, Cipponi A, Deveson IW, Santini NS, Kummerfeld S, Croucher PI, Marcellin E, Mercer TR. A universal molecular control for DNA, mRNA and protein expression. Nat Commun 2024; 15:2480. [PMID: 38509097 PMCID: PMC10954659 DOI: 10.1038/s41467-024-46456-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 02/28/2024] [Indexed: 03/22/2024] Open
Abstract
The expression of genes encompasses their transcription into mRNA followed by translation into protein. In recent years, next-generation sequencing and mass spectrometry methods have profiled DNA, RNA and protein abundance in cells. However, there are currently no reference standards that are compatible across these genomic, transcriptomic and proteomic methods, and provide an integrated measure of gene expression. Here, we use synthetic biology principles to engineer a multi-omics control, termed pREF, that can act as a universal molecular standard for next-generation sequencing and mass spectrometry methods. The pREF sequence encodes 21 synthetic genes that can be in vitro transcribed into spike-in mRNA controls, and in vitro translated to generate matched protein controls. The synthetic genes provide qualitative controls that can measure sensitivity and quantitative accuracy of DNA, RNA and peptide detection. We demonstrate the use of pREF in metagenome DNA sequencing and RNA sequencing experiments and evaluate the quantification of proteins using mass spectrometry. Unlike previous spike-in controls, pREF can be independently propagated and the synthetic mRNA and protein controls can be sustainably prepared by recipient laboratories using common molecular biology techniques. Together, this provides a universal synthetic standard able to integrate genomic, transcriptomic and proteomic methods.
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Affiliation(s)
- Helen M Gunter
- Australian Institute of Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland, Australia
- BASE mRNA Facility, The University of Queensland, Brisbane, Queensland, Australia
- ARC Centre of Excellence in Synthetic Biology, The University of Queensland, Brisbane, Queensland, Australia
| | - Scott E Youlten
- Department of Genetics, Yale University School of Medicine, New Haven, CT, 06510, USA
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- St Vincent's Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Andre L M Reis
- Genomics and Inherited Disease Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children's Research Institute, Sydney, New South Wales, Australia
- School of Electrical and Information Engineering, University of Sydney, Sydney, New South Wales, Australia
| | - Tim McCubbin
- Australian Institute of Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland, Australia
- ARC Centre of Excellence in Synthetic Biology, The University of Queensland, Brisbane, Queensland, Australia
| | - Bindu Swapna Madala
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children's Research Institute, Sydney, New South Wales, Australia
| | - Ted Wong
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Igor Stevanovski
- Genomics and Inherited Disease Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children's Research Institute, Sydney, New South Wales, Australia
| | - Arcadi Cipponi
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- St Vincent's Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Ira W Deveson
- Genomics and Inherited Disease Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children's Research Institute, Sydney, New South Wales, Australia
- School of Electrical and Information Engineering, University of Sydney, Sydney, New South Wales, Australia
| | - Nadia S Santini
- Centro Nacional de Investigación Disciplinaria en Conservación y Mejoramiento de Ecosistemas Forestales, INIFAP, Ciudad de México, 04010, Mexico
| | - Sarah Kummerfeld
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- St Vincent's Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Peter I Croucher
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- St Vincent's Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Esteban Marcellin
- Australian Institute of Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland, Australia
- ARC Centre of Excellence in Synthetic Biology, The University of Queensland, Brisbane, Queensland, Australia
| | - Tim R Mercer
- Australian Institute of Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland, Australia.
- BASE mRNA Facility, The University of Queensland, Brisbane, Queensland, Australia.
- ARC Centre of Excellence in Synthetic Biology, The University of Queensland, Brisbane, Queensland, Australia.
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia.
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