10 results on '"Jordan H. Whitlock"'
Search Results
2. Ten simple rules for using public biological data for your research
- Author
-
Vishal H. Oza, Jordan H. Whitlock, Elizabeth J. Wilk, Angelina Uno-Antonison, Brandon Wilk, Manavalan Gajapathy, Timothy C. Howton, Austyn Trull, Lara Ianov, Elizabeth A. Worthey, and Brittany N. Lasseigne
- Subjects
Biology (General) ,QH301-705.5 - Abstract
With an increasing amount of biological data available publicly, there is a need for a guide on how to successfully download and use this data. The 10 simple rules for using public biological data are: (1) use public data purposefully in your research; (2) evaluate data for your use case; (3) check data reuse requirements and embargoes; (4) be aware of ethics for data reuse; (5) plan for data storage and compute requirements; (6) know what you are downloading; (7) download programmatically and verify integrity; (8) properly cite data; (9) make reprocessed data and models Findable, Accessible, Interoperable, and Reusable (FAIR) and share; and (10) make pipelines and code FAIR and share. These rules are intended as a guide for researchers wanting to make use of available data and to increase data reuse and reproducibility.
- Published
- 2023
3. The precision medicine process for treating rare disease using the artificial intelligence tool mediKanren
- Author
-
Aleksandra Foksinska, Camerron M. Crowder, Andrew B. Crouse, Jeff Henrikson, William E. Byrd, Gregory Rosenblatt, Michael J. Patton, Kaiwen He, Thi K. Tran-Nguyen, Marissa Zheng, Stephen A. Ramsey, Nada Amin, John Osborne, UAB Precision Medicine Institute, Matthew Might, Stephen Barnes, Mei-Jan Chen, Mary E. Crumbley, Madeline Eckenrode, Crayton A. Fargason, Nathaniel Fehrmann, Forest Huls, Matthew Jarrell, Lindsay Jenkins, Meg McCalley, Tamsyn Osborn, Elizabeth Pollard, Sienna Rucka, Nicholas T. Southern, Jillian Tinglin, and Jordan H. Whitlock
- Subjects
rare disease ,precision medicine ,drug repurposing ,artificial intelligence ,biomedical reasoning ,Electronic computers. Computer science ,QA75.5-76.95 - Abstract
There are over 6,000 different rare diseases estimated to impact 300 million people worldwide. As genetic testing becomes more common practice in the clinical setting, the number of rare disease diagnoses will continue to increase, resulting in the need for novel treatment options. Identifying treatments for these disorders is challenging due to a limited understanding of disease mechanisms, small cohort sizes, interindividual symptom variability, and little commercial incentive to develop new treatments. A promising avenue for treatment is drug repurposing, where FDA-approved drugs are repositioned as novel treatments. However, linking disease mechanisms to drug action can be extraordinarily difficult and requires a depth of knowledge across multiple fields, which is complicated by the rapid pace of biomedical knowledge discovery. To address these challenges, The Hugh Kaul Precision Medicine Institute developed an artificial intelligence tool, mediKanren, that leverages the mechanistic insight of genetic disorders to identify therapeutic options. Using knowledge graphs, mediKanren enables an efficient way to link all relevant literature and databases. This tool has allowed for a scalable process that has been used to help over 500 rare disease families. Here, we provide a description of our process, the advantages of mediKanren, and its impact on rare disease patients.
- Published
- 2022
- Full Text
- View/download PDF
4. Genotype–phenotype correlations and novel molecular insights into the DHX30-associated neurodevelopmental disorders
- Author
-
Ilaria Mannucci, Nghi D. P. Dang, Hannes Huber, Jaclyn B. Murry, Jeff Abramson, Thorsten Althoff, Siddharth Banka, Gareth Baynam, David Bearden, Ana Beleza-Meireles, Paul J. Benke, Siren Berland, Tatjana Bierhals, Frederic Bilan, Laurence A. Bindoff, Geir Julius Braathen, Øyvind L. Busk, Jirat Chenbhanich, Jonas Denecke, Luis F. Escobar, Caroline Estes, Julie Fleischer, Daniel Groepper, Charlotte A. Haaxma, Maja Hempel, Yolanda Holler-Managan, Gunnar Houge, Adam Jackson, Laura Kellogg, Boris Keren, Catherine Kiraly-Borri, Cornelia Kraus, Christian Kubisch, Gwenael Le Guyader, Ulf W. Ljungblad, Leslie Manace Brenman, Julian A. Martinez-Agosto, Matthew Might, David T. Miller, Kelly Q. Minks, Billur Moghaddam, Caroline Nava, Stanley F. Nelson, John M. Parant, Trine Prescott, Farrah Rajabi, Hanitra Randrianaivo, Simone F. Reiter, Janneke Schuurs-Hoeijmakers, Perry B. Shieh, Anne Slavotinek, Sarah Smithson, Alexander P. A. Stegmann, Kinga Tomczak, Kristian Tveten, Jun Wang, Jordan H. Whitlock, Christiane Zweier, Kirsty McWalter, Jane Juusola, Fabiola Quintero-Rivera, Utz Fischer, Nan Cher Yeo, Hans-Jürgen Kreienkamp, and Davor Lessel
- Subjects
Medicine ,Genetics ,QH426-470 - Abstract
Abstract Background We aimed to define the clinical and variant spectrum and to provide novel molecular insights into the DHX30-associated neurodevelopmental disorder. Methods Clinical and genetic data from affected individuals were collected through Facebook-based family support group, GeneMatcher, and our network of collaborators. We investigated the impact of novel missense variants with respect to ATPase and helicase activity, stress granule (SG) formation, global translation, and their effect on embryonic development in zebrafish. SG formation was additionally analyzed in CRISPR/Cas9-mediated DHX30-deficient HEK293T and zebrafish models, along with in vivo behavioral assays. Results We identified 25 previously unreported individuals, ten of whom carry novel variants, two of which are recurrent, and provide evidence of gonadal mosaicism in one family. All 19 individuals harboring heterozygous missense variants within helicase core motifs (HCMs) have global developmental delay, intellectual disability, severe speech impairment, and gait abnormalities. These variants impair the ATPase and helicase activity of DHX30, trigger SG formation, interfere with global translation, and cause developmental defects in a zebrafish model. Notably, 4 individuals harboring heterozygous variants resulting either in haploinsufficiency or truncated proteins presented with a milder clinical course, similar to an individual harboring a de novo mosaic HCM missense variant. Functionally, we established DHX30 as an ATP-dependent RNA helicase and as an evolutionary conserved factor in SG assembly. Based on the clinical course, the variant location, and type we establish two distinct clinical subtypes. DHX30 loss-of-function variants cause a milder phenotype whereas a severe phenotype is caused by HCM missense variants that, in addition to the loss of ATPase and helicase activity, lead to a detrimental gain-of-function with respect to SG formation. Behavioral characterization of dhx30-deficient zebrafish revealed altered sleep-wake activity and social interaction, partially resembling the human phenotype. Conclusions Our study highlights the usefulness of social media to define novel Mendelian disorders and exemplifies how functional analyses accompanied by clinical and genetic findings can define clinically distinct subtypes for ultra-rare disorders. Such approaches require close interdisciplinary collaboration between families/legal representatives of the affected individuals, clinicians, molecular genetics diagnostic laboratories, and research laboratories.
- Published
- 2021
- Full Text
- View/download PDF
5. Nucleic acid liquid biopsies in Alzheimer's disease: current state, challenges, and opportunities
- Author
-
Tabea M. Soelter, Jordan H. Whitlock, Avery S. Williams, Andrew A. Hardigan, and Brittany N. Lasseigne
- Subjects
Liquid biopsy ,Circulating biomarkers ,Alzheimer's disease ,Neurodegeneration ,Cell-free ,Diagnosis ,Science (General) ,Q1-390 ,Social sciences (General) ,H1-99 - Abstract
Alzheimer's disease (AD) is the most common neurodegenerative disease and affects persons of all races, ethnic groups, and sexes. The disease is characterized by neuronal loss leading to cognitive decline and memory loss. There is no cure and the effectiveness of existing treatments is limited and depends on the time of diagnosis. The long prodromal period, during which patients' ability to live a normal life is not affected despite neuronal loss, often leads to a delayed diagnosis because it can be mistaken for normal aging of the brain. In order to make a substantial impact on AD patient survival, early diagnosis may provide a greater therapeutic window for future therapies to slow AD-associated neurodegeneration. Current gold standards for disease detection include magnetic resonance imaging and positron emission tomography scans, which visualize amyloid β and phosphorylated tau depositions and aggregates. Liquid biopsies, already an active field of research in precision oncology, are hypothesized to provide early disease detection through minimally or non-invasive sample collection techniques. Liquid biopsies in AD have been studied in cerebrospinal fluid, blood, ocular, oral, and olfactory fluids. However, most of the focus has been on blood and cerebrospinal fluid due to biomarker specificity and sensitivity attributed to the effects of the blood-brain barrier and inter-laboratory variation during sample collection. Many studies have identified amyloid β and phosphorylated tau levels as putative biomarkers, however, advances in next-generation sequencing-based liquid biopsy methods have led to significant interest in identifying nucleic acid species associated with AD from liquid tissues. Differences in cell-free RNAs and DNAs have been described as potential biomarkers for AD and hold the potential to affect disease diagnosis, treatment, and future research avenues.
- Published
- 2022
- Full Text
- View/download PDF
6. Biallelic MADD variants cause a phenotypic spectrum ranging from developmental delay to a multisystem disorder
- Author
-
Katherine Wesseling Perry, Archana Raja, Emilie D. Douine, Xue Zhong Liu, Brent L. Fogel, Stan F. Nelson, Kenneth R. Maravilla, Eva H. Baker, Dave Viskochil, Kerstin Kutsche, Jordan H. Whitlock, Susan L. Samson, Christine M. Eng, Chloe M. Reuter, Suman Jayadev, David R. Adams, Sihoun Hahn, Rebecca C. Spillmann, Margaret Adam, Heather C Mefford, John C. Carey, Ehsan Ghayoor Karimiani, Donna M. Krasnewich, David Goldstein, Susan A. Korrick, Guoyun Yu, Tomas Honzik, Henry Houlden, Andrea L. Gropman, David A. Sweetser, Anna Bican, Carlos A. Bacino, Liliana Fernandez, Gabrielle Brown, Justin Alvey, Hane Lee, Emanuele G. Coci, Hongzheng Dai, Mario Saporta, Laurel A. Cobban, John F. Bohnsack, Stephanie Fox, Heidi Cope, Tyra Estwick, Lorraine Potocki, Nichole Hayes, Elizabeth A. Burke, Rizwan Hamid, Aaron R. Quinlan, Kelly Hassey, Lindsay C. Burrage, Jane Juusola, Adeline Vanderver, Malik Alawi, Teri A. Manolio, Maja Hempel, Esther M. Maier, Jennifer Kennedy, Bruce D. Gelb, Martha Horike-Pyne, Amarilis Sanchez-Valle, Euan A. Ashley, Surendra Dasari, Elizabeth Blue, Eva Morava-Kozicz, Natalie Rosenwasser, Alan H. Beggs, Bryn D. Webb, Isaac S. Kohane, Kelly Schoch, C. Christopher Lau, Nicole M. Walley, Laura M. Amendola, Genecee Renteria, Catherine H. Sillari, Jonathan A. Bernstein, Pinar Bayrak-Toydemir, R. Frank Kooy, Mariko Nakano-Okuno, Manuela Siekmeyer, Marije E. C. Meuwissen, Stephanie Bivona, Mark Wener, Precilla D'Souza, Olveen Carrasquillo, Paolo Moretti, Diane B. Zastrow, David J. Eckstein, Janet S. Sinsheimer, Kathy Sisco, Holly K. Tabor, William E. Byrd, Esteban C. Dell'Angelica, Rosario Isasi, Jacinda B. Sampson, Carsten Bonnenmann, J. Lawrence Merritt, Joan M. Stoler, Richard L. Maas, Paul G. Fisher, Jeanette C. Papp, Kimberly LeBlanc, Lilianna Solnica-Krezel, Mustafa Tekin, Mathias Woidy, Andrew B. Crouse, Katleen Ballon, David Murphy, Matthew T. Wheeler, Joseph Loscalzo, Ellen Macnamara, Cecelia P. Tamburro, Lefkothea P. Karaviti, Chunli Zhao, Ingrid A. Holm, Pankaj B. Agrawal, Alana L. Grajewski, Stephen C. Pak, Ian R. Lanza, Mohammad Doosti, Jennifer E. Posey, Rebecca Signer, Katie Golden-Grant, Christopher A. Walsh, Alica M. Goldman, Jyoti G. Dayal, Queenie K.-G. Tan, Martin G. Martin, Joy D. Cogan, Kevin S. Smith, Deborah A. Nickerson, Elisabeth McGee, Laure Fresard, Rena A. Godfrey, Sharyn A. Lincoln, Kathleen E. Sullivan, Mariska Davids, Melissa A. Walker, Prashant Sharma, Maria Iascone, Neil H. Parker, Carlos Ferreira, Elizabeth L. Fieg, Edwin K. Silverman, Michael L. Cunningham, Pengfei Liu, Edward M. Behrens, Sandra K. Loo, David R. Murdock, F. Sessions Cole, C. Ron Scott, Dan Doherty, Elly Brokamp, John H. Newman, Alden Y. Huang, Laura A. Pace, Avi Nath, Jimmy Bennet, Georg Christoph Korenke, Alyssa A. Tran, Gabriel F. Batzli, Jimann Shin, Matthew A. Deardorff, Naghmeh Dorrani, Diane Beysen, Irma Gutierrez, Stanislav Kmoch, Majid Alfadhel, Fred F. Telischi, Jennifer A. Sullivan, William A. Gahl, María Palomares-Bralo, Gerard T. Berry, Colleen E. McCormack, Lance H. Rodan, Reza Maroofian, Lenka Nosková, Judy Schaechter, Lynne A. Wolfe, Deborah Krakow, Daryl A. Scott, Tara Wenger, Jason Hom, Dustin Baldridge, Lynette Rives, Lee-kai Wang, Dawn L. Earl, Ralph L. Sacco, Fernando Santos-Simarro, Irman Forghani, Fuki M. Hisama, Terra R. Coakley, Hsiao-Tuan Chao, Jeremy D. Woods, Emily G. Kelley, Jean M. Johnston, Neil A. Hanchard, Amy K. Robertson, Matt Velinder, Byron L. Lam, Wendy H. Raskind, William J. Craigen, Stephan Züchner, Guney Bademci, Julian A. Martinez-Agosto, Mary Koziura, Beth A. Martin, Angela Sun, John A. Phillips, Seema R. Lalani, Daniela Buhas, Emily Solem, Gary D. Clark, Gill Bejerano, Ingo Kurth, Deborah Barbouth, Tiina K. Urv, Fanny Kortüm, Ian A. Glass, Ta Chen Peter Chang, Yong Huang, Roy C. Levitt, Paola Francesca Ajmone, Brenna Boyd, René Santer, Tim Schedl, David D. Draper, Ghayda M. Mirzaa, Aroa Rodríguez Alonso, Stephanie Wallace, Colleen E. Wahl, Calum A. MacRae, Gail P. Jarvik, Jacob L. McCauley, Jill A. Rosenfeld, Ronit Marom, Monte Westerfield, Matthew Might, Poupak Javaher-Haghighi, Brendan C. Lanpher, Devon Bonner, Cynthia J. Tifft, Cecilia Esteves, May Christine V. Malicdan, Jim Bale, Fariha Jamal, Nicola Longo, Christina G.S. Palmer, Lisa Emrick, Peter H. Byers, Vandana Shashi, Tiphanie P. Vogel, Richard A. Lewis, Jijun Wan, Barbara N. Pusey, Maria T. Acosta, Jaak Jaeken, Allyn McConkie-Rosell, Shirley Sutton, John Yang, Lorenzo D. Botto, Hilde Peeters, Rong Mao, Catherine Groden, Brendan Lee, Marta M. Majcherska, Rami Abou Jamra, Ashok Balasubramanyam, Joel B. Krier, Majid Mojarrad, Maria Francesca Bedeschi, Mahshid S. Azamian, Shruti Marwaha, Heather A. Colley, Katrina M. Dipple, Sirisak Chanprasert, Alexa T. McCray, Nicholas Stong, Anne V. Hing, Laura A. Mamounas, Edward C. Smith, Lauren C. Briere, John J.E. Mulvihill, Virginia P. Sybert, Maura R.Z. Ruzhnikov, Valerie Maduro, Frances A. High, Manish J. Butte, Willa Thorson, J. Carl Pallais, Jennefer N. Kohler, Dana Kiley, Raphael Bernier, Christina Lam, Michael J. Bamshad, Patricia A. Ward, Michael F. Wangler, Anita E. Beck, Shinya Yamamoto, Beverly Berg-Rood, Robb Rowley, Gabor T. Marth, Cynthia M. Cooper, Jeffrey G. Jarvik, Thomas C. Markello, Saskia Biskup, Devin Oglesbee, Laura Duncan, Elijah Kravets, Daniel J. Wegner, Mercedes E. Alejandro, Sarah K. Nicholas, Jennifer A. Wambach, Marni J. Falk, Brianna M. Tucker, Marie Morimoto, Corina Heller, Donna Novacic, Camilo Toro, Ashley Andrews, James P. Orengo, Shweta U. Dhar, and Pauline E. Schneeberger
- Subjects
0301 basic medicine ,MAPK/ERK pathway ,Death Domain Receptor Signaling Adaptor Proteins ,Programmed cell death ,Developmental Disabilities ,Biology ,03 medical and health sciences ,0302 clinical medicine ,Epidermal growth factor ,medicine ,Guanine Nucleotide Exchange Factors ,Humans ,Death domain ,Kinase ,Original Articles ,Phenotype ,Hypotonia ,Protein Transport ,030104 developmental biology ,Mutation ,Cancer research ,Human medicine ,Neurology (clinical) ,Nervous System Diseases ,Signal transduction ,medicine.symptom ,030217 neurology & neurosurgery ,Signal Transduction - Abstract
In pleiotropic diseases, multiple organ systems are affected causing a variety of clinical manifestations. Here, we report a pleiotropic disorder with a unique constellation of neurological, endocrine, exocrine, and haematological findings that is caused by biallelic MADD variants. MADD, the mitogen-activated protein kinase (MAPK) activating death domain protein, regulates various cellular functions, such as vesicle trafficking, activity of the Rab3 and Rab27 small GTPases, tumour necrosis factor-α (TNF-α)-induced signalling and prevention of cell death. Through national collaboration and GeneMatcher, we collected 23 patients with 21 different pathogenic MADD variants identified by next-generation sequencing. We clinically evaluated the series of patients and categorized the phenotypes in two groups. Group 1 consists of 14 patients with severe developmental delay, endo- and exocrine dysfunction, impairment of the sensory and autonomic nervous system, and haematological anomalies. The clinical course during the first years of life can be potentially fatal. The nine patients in Group 2 have a predominant neurological phenotype comprising mild-to-severe developmental delay, hypotonia, speech impairment, and seizures. Analysis of mRNA revealed multiple aberrant MADD transcripts in two patient-derived fibroblast cell lines. Relative quantification of MADD mRNA and protein in fibroblasts of five affected individuals showed a drastic reduction or loss of MADD. We conducted functional tests to determine the impact of the variants on different pathways. Treatment of patient-derived fibroblasts with TNF-α resulted in reduced phosphorylation of the extracellular signal-regulated kinases 1 and 2, enhanced activation of the pro-apoptotic enzymes caspase-3 and -7 and increased apoptosis compared to control cells. We analysed internalization of epidermal growth factor in patient cells and identified a defect in endocytosis of epidermal growth factor. We conclude that MADD deficiency underlies multiple cellular defects that can be attributed to alterations of TNF-α-dependent signalling pathways and defects in vesicular trafficking. Our data highlight the multifaceted role of MADD as a signalling molecule in different organs and reveal its physiological role in regulating the function of the sensory and autonomic nervous system and endo- and exocrine glands.
- Published
- 2020
- Full Text
- View/download PDF
7. Liquid biopsies in epilepsy: biomarkers for etiology, diagnosis, prognosis, and therapeutics
- Author
-
Jordan H. Whitlock, Tabea M. Soelter, Brittany N. Lasseigne, Avery S. Williams, and Andrew A. Hardigan
- Subjects
Cancer Research ,medicine.medical_specialty ,Circulating biomarkers ,medicine.medical_treatment ,Reproductive medicine ,Context (language use) ,Review Article ,Bioinformatics ,Epilepsy ,Multiple time ,medicine ,Humans ,Sampling (medicine) ,Liquid biopsy ,business.industry ,other ,Cell-free ,Cell Biology ,medicine.disease ,Nucleic acids ,Etiology ,RNA ,Sample collection ,business ,Vagus nerve stimulation ,Biomarkers - Abstract
Epilepsy is one of the most common diseases of the central nervous system, impacting nearly 50 million people around the world. Heterogeneous in nature, epilepsy presents in children and adults alike. Currently, surgery is one treatment approach that can completely cure epilepsy. However, not all individuals are eligible for surgical procedures or have successful outcomes. In addition to surgical approaches, antiepileptic drugs (AEDs) have also allowed individuals with epilepsy to achieve freedom from seizures. Others have found treatment through nonpharmacologic approaches such as vagus nerve stimulation, or responsive neurostimulation. Difficulty in accessing samples of human brain tissue along with advances in sequencing technology have driven researchers to investigate sampling liquid biopsies in blood, serum, plasma, and cerebrospinal fluid within the context of epilepsy. Liquid biopsies provide minimal or non-invasive sample collection approaches and can be assayed relatively easily across multiple time points, unlike tissue-based sampling. Various efforts have investigated circulating nucleic acids from these samples including microRNAs, cell-free DNA, transfer RNAs, and long non-coding RNAs. Here, we review nucleic acid-based liquid biopsies in epilepsy to improve understanding of etiology, diagnosis, prediction, and therapeutic monitoring.
- Published
- 2021
8. Nucleic Acid Liquid Biopsies in Alzheimer’s Disease: Current State, Challenges, and Opportunities
- Author
-
Brittany N. Lasseigne, Tabea M. Soelter, Jordan H. Whitlock, Andrew A. Hardigan, and Avery S. Williams
- Subjects
general_medical_research ,Cell-free fetal DNA ,business.industry ,Nucleic acid ,Cancer research ,Medicine ,Disease ,Current (fluid) ,Liquid biopsy ,business - Abstract
Alzheimer’s disease is the most common neurodegenerative disease and affects persons of all races, ethnic groups, and sexes. The disease is characterized by neuronal loss leading to cognitive decline and memory loss. There is no cure and the effectiveness of existing treatments is limited and depends on the time of diagnosis. The long prodromal period, during which patients’ ability to live a normal life is not affected despite neuronal loss, often leads to a delayed diagnosis because it can be mistaken for normal aging of the brain. In order to make a substantial impact on AD patients, early diagnosis may provide a greater therapeutic window for future therapies to slow AD-associated neurodegeneration. Current gold standards for disease detection include magnetic resonance imaging and positron emission tomography scans, which visualize amyloid β and phosphorylated tau depositions and aggregates. Liquid biopsies, already an active field of research in precision oncology, are hypothesized to provide early disease detection through minimally or non-invasive sample collection techniques. Liquid biopsies in Alzheimer’s disease have been studied in cerebrospinal fluid, blood, ocular, oral, and olfactory fluids. However, most of the focus has been on blood and cerebrospinal fluid due to biomarker specificity and sensitivity attributed to the effects of the blood-brain barrier and inter-laboratory variation during sample collection. Many studies have identified amyloid β and phosphorylated tau levels as putative biomarkers, however, advances in next-generation sequencing-based liquid biopsy methods have led to significant interest in identifying nucleic acids species associated with Alzheimer’s disease from liquid tissues. Differences in cell-free RNAs and DNAs have been described as potential biomarkers for AD and hold the potential to affect disease diagnosis, treatment, and future research avenues.
- Published
- 2021
- Full Text
- View/download PDF
9. Nucleic acid liquid biopsies in Alzheimer's disease: current state, challenges, and opportunities
- Author
-
Tabea M. Soelter, Jordan H. Whitlock, Avery S. Williams, Andrew A. Hardigan, and Brittany N. Lasseigne
- Subjects
Multidisciplinary - Abstract
Alzheimer's disease (AD) is the most common neurodegenerative disease and affects persons of all races, ethnic groups, and sexes. The disease is characterized by neuronal loss leading to cognitive decline and memory loss. There is no cure and the effectiveness of existing treatments is limited and depends on the time of diagnosis. The long prodromal period, during which patients' ability to live a normal life is not affected despite neuronal loss, often leads to a delayed diagnosis because it can be mistaken for normal aging of the brain. In order to make a substantial impact on AD patient survival, early diagnosis may provide a greater therapeutic window for future therapies to slow AD-associated neurodegeneration. Current gold standards for disease detection include magnetic resonance imaging and positron emission tomography scans, which visualize amyloid β and phosphorylated tau depositions and aggregates. Liquid biopsies, already an active field of research in precision oncology, are hypothesized to provide early disease detection through minimally or non-invasive sample collection techniques. Liquid biopsies in AD have been studied in cerebrospinal fluid, blood, ocular, oral, and olfactory fluids. However, most of the focus has been on blood and cerebrospinal fluid due to biomarker specificity and sensitivity attributed to the effects of the blood-brain barrier and inter-laboratory variation during sample collection. Many studies have identified amyloid β and phosphorylated tau levels as putative biomarkers, however, advances in next-generation sequencing-based liquid biopsy methods have led to significant interest in identifying nucleic acid species associated with AD from liquid tissues. Differences in cell-free RNAs and DNAs have been described as potential biomarkers for AD and hold the potential to affect disease diagnosis, treatment, and future research avenues.
- Published
- 2021
10. Genotype–phenotype correlations and novel molecular insights into the DHX30-associated neurodevelopmental disorders
- Author
-
Alexander P.A. Stegmann, Jun Wang, Anne Slavotinek, Cornelia Kraus, Paul J. Benke, Christiane Zweier, Fabiola Quintero-Rivera, Øyvind L. Busk, Kirsty McWalter, Hans-Jürgen Kreienkamp, Luis F. Escobar, Geir J. Braathen, Kristian Tveten, Farrah Rajabi, Charlotte A. Haaxma, David Bearden, John M. Parant, Yolanda Holler-Managan, Nghi Dang, Leslie Manace Brenman, Ana Beleza, Thorsten Althoff, Cathy Kiraly-Borri, Maja Hempel, Christian Kubisch, Kelly Q. Minks, Laura Kellogg, Hannes Huber, Ulf W. Ljungblad, Hanitra Randrianaivo, Perry B. Shieh, Jeff Abramson, Jirat Chenbhanich, Jonas Denecke, Billur Moghaddam, Gareth Baynam, Kinga K. Tomczak, Matthew Might, Jane Juusola, Jordan H. Whitlock, Gunnar Houge, Julie Fleischer, Laurence A. Bindoff, Siren Berland, Tatjana Bierhals, Adam Jackson, Gwenaël Le Guyader, Stanley F. Nelson, Caroline Estes, Nan Cher Yeo, Simone F. Reiter, Utz Fischer, Sarah F. Smithson, Daniel Groepper, Siddharth Banka, Davor Lessel, Frédéric Bilan, Ilaria Mannucci, Trine Prescott, David T. Miller, Janneke H M Schuurs-Hoeijmakers, Boris Keren, Jaclyn B. Murry, Caroline Nava, and Julian A. Martinez-Agosto
- Subjects
Genetics ,medicine.medical_specialty ,biology ,medicine.disease ,biology.organism_classification ,RNA Helicase A ,Phenotype ,Neurodevelopmental disorder ,Molecular genetics ,medicine ,Missense mutation ,Global developmental delay ,Haploinsufficiency ,Zebrafish - Abstract
BackgroundWe aimed to define the clinical and mutational spectrum, and to provide novel molecular insights into DHX30-associated neurodevelopmental disorder.MethodsClinical and genetic data from affected individuals were collected through family support group, GeneMatcher and our network of collaborators. We investigated the impact of novel missense variants with respect to ATPase and helicase activity, stress granule (SG) formation, global translation, and their effect on embryonic development in zebrafish. SG formation was additionally analyzed in CRISPR/Cas9-mediated DHX30-deficient HEK293T and zebrafish models, along with in vivo behavioral assays.ResultsWe identified 25 previously unreported individuals, ten of whom carry novel variants, two of which are recurrent, and provide evidence of gonadal mosaicism in one family. All 19 individuals harboring heterozygous missense variants within helicase core motifs (HCMs) have global developmental delay, intellectual disability, severe speech impairment and gait abnormalities. These variants impair the ATPase and helicase activity of DHX30, trigger SG formation, interfere with global translation, and cause developmental defects in a zebrafish model. Notably, 4 individuals harboring heterozygous variants resulting either in haploinsufficiency or truncated proteins presented with a milder clinical course, similar to an individual bearing a de novo mosaic HCM missense variant. Functionally, we established DHX30 as an ATP-dependent RNA helicase and as an evolutionary conserved factor in SG assembly. Based on the clinical course, the variant location and type we establish two distinct clinical subtypes. DHX30 loss-of-function mutations cause a milder phenotype whereas a severe phenotype is caused by HCM missense mutations that, in addition to the loss of ATPase and helicase activity, lead to a detrimental gain-of function with respect to SG formation. Behavioral characterization of dhx30 deficient zebrafish revealed altered sleep-wake activity and social interaction, partially resembling the human phenotype.ConclusionsOur study highlights the usefulness of social media in order to define novel Mendelian disorders, and exemplifies how functional analyses accompanied by clinical and genetic findings can define clinically distinct subtypes for ultra-rare disorders. Such approaches require close interdisciplinary collaboration between families/legal representatives of the affected individuals, clinicians, molecular genetics diagnostic laboratories and research laboratories.
- Published
- 2020
- Full Text
- View/download PDF
Catalog
Discovery Service for Jio Institute Digital Library
For full access to our library's resources, please sign in.