Gloria I. Perez, David Broadbent, Ahmed A. Zarea, Benedikt Dolgikh, Matthew P. Bernard, Alicia Withrow, Amelia McGill, Victoria Toomajian, Lukose K. Thampy, Jack Harkema, Joel R. Walker, Thomas A. Kirkland, Michael H. Bachmann, Jens Schmidt, Masamitsu Kanada
{"title":"In Vitro and In Vivo Analysis of Extracellular Vesicle-Mediated Metastasis Using a Bright, Red-Shifted Bioluminescent Reporter Protein (Advanced Genetics 1/03)","authors":"Gloria I. Perez, David Broadbent, Ahmed A. Zarea, Benedikt Dolgikh, Matthew P. Bernard, Alicia Withrow, Amelia McGill, Victoria Toomajian, Lukose K. Thampy, Jack Harkema, Joel R. Walker, Thomas A. Kirkland, Michael H. Bachmann, Jens Schmidt, Masamitsu Kanada","doi":"10.1002/ggn2.202270011","DOIUrl":"10.1002/ggn2.202270011","url":null,"abstract":"<p><b>Extracellular Vesicle Imaging</b></p><p>Cancer cell-derived extracellular vesicles (EVs) promote tumor growth and spread. Studying the distribution of EVs in the body is key to understanding cancer progression and developing therapies. In article number 2100055, Masamitsu Kanada and co-workers develop a highly sensitive EV reporter for tracking heterogeneous EV populations released from cancer cells in live mice.\u0000\u0000 <figure>\u0000 <div><picture>\u0000 <source></source></picture><p></p>\u0000 </div>\u0000 </figure></p>","PeriodicalId":72071,"journal":{"name":"Advanced genetics (Hoboken, N.J.)","volume":"3 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/ggn2.202270011","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76186053","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Masthead: (Advanced Genetics 1/03)","authors":"","doi":"10.1002/ggn2.202270012","DOIUrl":"10.1002/ggn2.202270012","url":null,"abstract":"Nadav Ahituv, University of California, San Francisco, San Francisco, CA USA Nir Barzilai, Albert Einstein College of Medicine, Bronx, NY USA Jacqueline Batley, University of Western Australia, Perth, Australia Touati Benoukraf,Memorial University of Newfoundland, St. John’s, NL, Canada Ewan Birney, EMBL-EBI, Cambridge, UK Catherine A. Brownstein, Boston Children’s Hospital, Boston, MA USA Stephen J. Chanock, National Cancer Institute, Bethesda, MD USA George Church, Harvard Medical School, Boston, MA USA Francesco Cucca, University of Sassari, Sassari, Sardinia, Italy Marcella Devoto, Children’s Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA USA Roland Eils, Berlin Institue of Health, Berlin, Germany Jeanette Erdmann, Institute for Cardiogenetics, University of Lubeck, Lubeck, Germany Andrew Feinberg, Johns Hopkins University, Baltimore, MD USA Claudio Franceschi, University of Bologna, Bologna, Italy Paul W. Franks, Lund University, Malmö, Sweden Rachel Freathy, University of Exeter, Exeter, UK Jingyuan Fu, University Medical Center Groningen, Groningen, The Netherlands Eileen Furlong, European Molecular Biology Laboratory, Heidelberg, Germany Tom Gilbert, University of Copenhagen, The Globe Institute, Copenhagen, Denmark Joseph G. Gleeson, University of California, San Diego, Howard Hughes Medical Institute for Genomic Medicine, La Jolla, CA USA Erica Golemis, Fox Chase Cancer Center, Philadelphia, PA USA Sarah Hearne, International Maize and Wheat Improvement Centre (CIMMYT), Texcoco, Mexico Agnar Helgason, deCODE Genetics, Reykjavik, Iceland Kristina Hettne, Leiden University Libraries, Leiden, The Netherlands John Hickey, The Roslin Institute, Edinburgh, UK Sanwen Huang, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China Youssef Idaghdour, New York University, Abu Dhabi, Abu Dhabi, UAE Rosalind John, Cardiff University, Cardiff, UK Astrid Junker, Leibniz Institute of Plant Genetics, Crop Plant Research (IPK) Gatersleben, Stadt Seeland, OT Gatersleben, Germany Moien Kanaan, Bethlehem University, Bethlehem, Palestine Beat Keller, University of Zurich, Zurich, Switzerland Tuuli Lappalainen, New York Genome Center, Columbia University, New York, NY USA Luis F. Larrondo, Pontifica Universidad Catolica de Chile, Santiago, Chile Suet-Yi Leung, The University of Hong Kong, Hong Kong, China Ryan Lister, The University of Western Australia, Perth, Australia Jianjun Liu, Genome Institute Singapore, Singapore Naomichi Matsumoto, Yokohama City University, Yokohama, Japan Rachel S. Meyer, University of California, Los Angeles, Los Angeles, CA USA Nicola Mulder, University of Cape Town, Cape Town, South Africa Huck-Hui Ng, Genome Institute of Singapore, Singapore John Novembre, University of Chicago, Chicago, IL USA Seishi Ogawa, Kyoto University, Kyoto, Japan Guilherme Oliveira, Vale Institute of Technology, Belem, Brazil Qiang Pan-Hammarstrom, Karolinska Institute, Stockholm, Sw","PeriodicalId":72071,"journal":{"name":"Advanced genetics (Hoboken, N.J.)","volume":"3 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/ggn2.202270012","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87759173","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Genetics of Ataxias in Indian Population: A Collative Insight from a Common Genetic Screening Tool","authors":"Pooja Sharma, Akhilesh Kumar Sonakar, Nishu Tyagi, Varun Suroliya, Manish Kumar, Rintu Kutum, Vivekananda Asokchandran, Sakshi Ambawat, Uzma Shamim, Avni Anand, Ishtaq Ahmad, Sunil Shakya, Bharathram Uppili, Aradhana Mathur, Shaista Parveen, Shweta Jain, Jyotsna Singh, Malika Seth, Sana Zahra, Aditi Joshi, Divya Goel, Shweta Sahni, Asangla Kamai, Saruchi Wadhwa, Aparna Murali, Sheeba Saifi, Debashish Chowdhury, Sanjay Pandey, Kuljeet Singh Anand, Ranganathan Lakshmi Narasimhan, Sanghamitra Laskar, Suman Kushwaha, Mukesh Kumar, Cheruvallill Velayudhan Shaji, Madakasira Vasantha Padma Srivastava, Achal K. Srivastava, Mohammed Faruq, GOMED-Ataxia study group","doi":"10.1002/ggn2.202100078","DOIUrl":"10.1002/ggn2.202100078","url":null,"abstract":"<p>Cerebellar ataxias (CAs) represent a group of autosomal dominant and recessive neurodegenerative disorders affecting cerebellum with or without spinal cord. Overall, CAs have preponderance for tandem nucleotide repeat expansions as an etiological factor (10 TREs explain nearly 30–40% of ataxia cohort globally). The experience of 10 years of common genetic ataxia subtypes for ≈5600 patients’ referrals (Pan-India) received at a single center is shared herein. Frequencies (in %, n) of SCA types and FRDA in the sample cohort are observed as follows: SCA12 (8.6%, 490); SCA2 (8.5%, 482); SCA1 (4.8%, 272); SCA3 (2%, 113); SCA7 (0.5%, 28); SCA6 (0.1%, 05); SCA17 (0.1%, 05), and FRDA (2.2%, 127). A significant amount of variability in TRE lengths at each locus is observed, we noted presence of biallelic expansion, co-occurrence of SCA-subtypes, and the presence of premutable normal alleles. The frequency of mutated GAA-FRDA allele in healthy controls is 1/158 (0.63%), thus an expected FRDA prevalence of 1:100 000 persons. The data of this study are relevant not only for clinical decision making but also for guidance in direction of genetic investigations, transancestral comparison of genotypes, and lastly provide insight for policy decision for the consideration of SCAs under rare disease category.</p>","PeriodicalId":72071,"journal":{"name":"Advanced genetics (Hoboken, N.J.)","volume":"3 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-03-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9744545/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10498433","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Jimmy Phuong, Naomi O. Riches, Charisse Madlock-Brown, Deborah Duran, Luca Calzoni, Juan C. Espinoza, Gora Datta, Ramakanth Kavuluru, Nicole G. Weiskopf, Cavin K. Ward-Caviness, Asiyah Yu Lin
{"title":"Social Determinants of Health Factors for Gene–Environment COVID-19 Research: Challenges and Opportunities","authors":"Jimmy Phuong, Naomi O. Riches, Charisse Madlock-Brown, Deborah Duran, Luca Calzoni, Juan C. Espinoza, Gora Datta, Ramakanth Kavuluru, Nicole G. Weiskopf, Cavin K. Ward-Caviness, Asiyah Yu Lin","doi":"10.1002/ggn2.202100056","DOIUrl":"10.1002/ggn2.202100056","url":null,"abstract":"<p>The characteristics of a person's health status are often guided by how they live, grow, learn, their genetics, as well as their access to health care. Yet, all too often, studies examining the relationship between social determinants of health (behavioral, sociocultural, and physical environmental factors), the role of demographics, and health outcomes poorly represent these relationships, leading to misinterpretations, limited study reproducibility, and datasets with limited representativeness and secondary research use capacity. This is a profound hurdle in what questions can or cannot be rigorously studied about COVID-19. In practice, gene–environment interactions studies have paved the way for including these factors into research. Similarly, our understanding of social determinants of health continues to expand with diverse data collection modalities as health systems, patients, and community health engagement aim to fill the knowledge gaps toward promoting health and wellness. Here, a conceptual framework is proposed, adapted from the population health framework, socioecological model, and causal modeling in gene–environment interaction studies to integrate the core constructs from each domain with practical considerations needed for multidisciplinary science.</p>","PeriodicalId":72071,"journal":{"name":"Advanced genetics (Hoboken, N.J.)","volume":"3 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-03-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9087427/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10325303","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Rajneesh Kaur, Cassandra McDonald, Bettina Meiser, Finlay Macrae, Sian K Smith, Yoon Jung Kang, Michael Caruana, Gillian Mitchell
{"title":"The Risk-Reducing Effect of Aspirin in Lynch Syndrome Carriers: Development and Evaluation of an Educational Leaflet","authors":"Rajneesh Kaur, Cassandra McDonald, Bettina Meiser, Finlay Macrae, Sian K Smith, Yoon Jung Kang, Michael Caruana, Gillian Mitchell","doi":"10.1002/ggn2.202100046","DOIUrl":"10.1002/ggn2.202100046","url":null,"abstract":"<p>Carriers of germline mutations in genes associated with Lynch syndrome are at increased risk for colorectal, endometrial, ovarian, and other cancers. There is evidence that daily consumption of aspirin may reduce cancer risk in these individuals. There is a need for educational resources to inform carriers of the risk-reducing effects of aspirin or to support decision-making. An educational leaflet describing the risks and benefits of using aspirin as risk-reducing medicine in carriers of Lynch-syndrome-related mutations is developed and pilot tested in 2017. Carriers are ascertained through a familial cancer clinic and surveyed using a mailed, self-administered questionnaire. The leaflet is highly rated for its content, clarity, length, relevance, and visual appeal by more than 70% of the participants. Most participants (91%) report “a lot” or “quite a bit” of improvement in perceived understanding in knowledge about who might benefit from taking aspirin, its benefits, how long to take it, the reduction in bowel cancer risk, and the optimal dosage. A few (14%) participants seek more information on the dosage of aspirin. This leaflet will be useful as an aid to facilitate discussion between patients and their health care professionals about the use of aspirin as a risk-reducing medication.</p>","PeriodicalId":72071,"journal":{"name":"Advanced genetics (Hoboken, N.J.)","volume":"3 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9744515/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10498430","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Single-Cell Transcriptome Identifies Drug-Resistance Signature and Immunosuppressive Microenvironment in Metastatic Small Cell Lung Cancer","authors":"Jing Zhang, Haiping Zhang, Lele Zhang, Dianke Li, Mengfan Qi, Liping Zhang, Huansha Yu, Di Wang, Gening Jiang, Xujun Wang, Xianmin Zhu, Peng Zhang","doi":"10.1002/ggn2.202100060","DOIUrl":"10.1002/ggn2.202100060","url":null,"abstract":"<p>Small cell lung cancer (SCLC) is a deadly neuroendocrine malignancy with high metastasis. However, the heterogeneity of metastatic SCLC at the single-cell level remains elusive. The single-cell transcriptome of a total of 24 081 cells in metastatic lymph node samples from seven SCLC patients via endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) is examined. Genomic alterations are also examined by whole exome sequencing (WES) and the immune infiltration between SCLC and non-SCLC (NSCLC) is compared using public single-cell RNA sequencing (scRNA-seq) data. It is identified that malignant cells in lymph-node metastatic SCLC have inter-patient and intra-tumor heterogeneity characterized by distinct <i>ASCL1</i> and <i>NEUROD1</i> expression patterns. High expression of genes such as <i>FZD8</i> in WNT pathway is associated with drug resistance in malignant cells. Compared to NSCLC, SCLC harbors a unique immunosuppressive tumor microenvironment. Malignant cells exhibit a pattern of attenuated MHC-I antigen presentation-related gene expression, which is associated with relatively low proportion of exhausted T cells. Natural killer (NK) cells display impaired antitumor function with high expression of <i>TGFBR2</i>. This work characterizes the inter-patient and intra-tumor heterogeneity of metastatic SCLC and uncovers the exhaustion signatures in NK cells, which may pave the way for novel treatments for SCLC including immune checkpoint blockade-based immunotherapy.</p>","PeriodicalId":72071,"journal":{"name":"Advanced genetics (Hoboken, N.J.)","volume":"3 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9744506/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10498434","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Hanah Goetz, Austin Stone, Rong Zhang, Ying-Cheng Lai, Xiao-Jun Tian
{"title":"Double-Edged Role of Resource Competition in Gene Expression Noise and Control","authors":"Hanah Goetz, Austin Stone, Rong Zhang, Ying-Cheng Lai, Xiao-Jun Tian","doi":"10.1002/ggn2.202100050","DOIUrl":"10.1002/ggn2.202100050","url":null,"abstract":"Despite extensive investigation demonstrating that resource competition can significantly alter the circuits’ deterministic behaviors, a fundamental issue is how resource competition contributes to the gene expression noise and how the noise can be controlled. Utilizing a two-gene circuit as a prototypical system, we uncover a surprising double-edged role of resource competition in gene expression noise: the competition decreases noise through a resource constraint but generates its own type of noise which we name as “resource competitive noise.” Utilization of orthogonal resources enables retaining the noise reduction conferred by resource constraint while removing the added resource competitive noise. The noise reduction effects are studied using three negative feedback controller types: negatively competitive regulation (NCR), local, and global controllers, each having four placement architectures in the protein biosynthesis pathway (mRNA or protein inhibition on transcription or translation). Our results show that both local and NCR controllers with mRNA-mediated inhibition are efficacious at reducing noise, with NCR controllers demonstrating a superior noise-reduction capability. We also find that combining negative feedback controllers with orthogonal resources can improve the local controllers. This work provides deep insights into the origin of stochasticity in gene circuits with resource competition and guidance for developing effective noise control strategies.","PeriodicalId":72071,"journal":{"name":"Advanced genetics (Hoboken, N.J.)","volume":"3 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-02-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9390979/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40626316","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Gloria I. Perez, David Broadbent, Ahmed A. Zarea, Benedikt Dolgikh, Matthew P. Bernard, Alicia Withrow, Amelia McGill, Victoria Toomajian, Lukose K. Thampy, Jack Harkema, Joel R. Walker, Thomas A. Kirkland, Michael H. Bachmann, Jens Schmidt, Masamitsu Kanada
{"title":"In Vitro and In Vivo Analysis of Extracellular Vesicle-Mediated Metastasis Using a Bright, Red-Shifted Bioluminescent Reporter Protein","authors":"Gloria I. Perez, David Broadbent, Ahmed A. Zarea, Benedikt Dolgikh, Matthew P. Bernard, Alicia Withrow, Amelia McGill, Victoria Toomajian, Lukose K. Thampy, Jack Harkema, Joel R. Walker, Thomas A. Kirkland, Michael H. Bachmann, Jens Schmidt, Masamitsu Kanada","doi":"10.1002/ggn2.202100055","DOIUrl":"10.1002/ggn2.202100055","url":null,"abstract":"<p>Cancer cells produce heterogeneous extracellular vesicles (EVs) as mediators of intercellular communication. This study focuses on a novel method to image EV subtypes and their biodistribution in vivo. A red-shifted bioluminescence resonance energy transfer (BRET) EV reporter is developed, called PalmReNL, which allows for highly sensitive EV tracking in vitro and in vivo. PalmReNL enables the authors to study the common surface molecules across EV subtypes that determine EV organotropism and their functional differences in cancer progression. Regardless of injection routes, whether retro-orbital or intraperitoneal, PalmReNL positive EVs, isolated from murine mammary carcinoma cells, localized to the lungs. The early appearance of metastatic foci in the lungs of mammary tumor-bearing mice following multiple intraperitoneal injections of the medium and large EV (m/lEV)-enriched fraction derived from mammary carcinoma cells is demonstrated. In addition, the results presented here show that tumor cell-derived m/lEVs act on distant tissues through upregulating LC3 expression within the lung.</p>","PeriodicalId":72071,"journal":{"name":"Advanced genetics (Hoboken, N.J.)","volume":"3 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-01-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9744575/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10857981","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"A phylogenetic analysis of the wild Tulipa species (Liliaceae) of Kosovo based on plastid and nuclear DNA sequence","authors":"Avni Hajdari, Bledar Pulaj, Corinna Schmiderer, Xhavit Mala, Brett Wilson, Kimete Lluga-Rizani, Behxhet Mustafa","doi":"10.1002/ggn2.202100057","DOIUrl":"https://doi.org/10.1002/ggn2.202100057","url":null,"abstract":"<p><i>Adv. Genet</i>. <b>2021</b>, <i>2</i>, 2100016</p><p>https://doi.org/10.1002/ggn2.202100016</p><p>In the original version of this article, the name of the fourth author was spelled incorrectly. The correct spelling for the fourth author is Xhavit Mala. This was amended in the manuscript on December 01, 2021.</p>","PeriodicalId":72071,"journal":{"name":"Advanced genetics (Hoboken, N.J.)","volume":"2 4","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-12-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/ggn2.202100057","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"91859672","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}