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1. Heterozygous loss-of-function variants significantly expand the phenotypes associated with loss of GDF11

Author

Thomas A. Ravenscroft, Jennifer B. Phillips, Elizabeth Fieg, Sameer S. Bajikar, Judy Peirce, Jeremy Wegner, Alia A. Luna, Eric J. Fox, Yi-Lin Yan, Jill A. Rosenfeld, Jonathan Zirin, Oguz Kanca, Maria T. Acosta, Margaret Adam, David R. Adams, Pankaj B. Agrawal, Mercedes E. Alejandro, Justin Alvey, Laura Amendola, Ashley Andrews, Euan A. Ashley, Mahshid S. Azamian, Carlos A. Bacino, Guney Bademci, Eva Baker, Ashok Balasubramanya, Dustin Baldridge, Jim Bale, Michael Bamshad, Deborah Barbouth, Pinar Bayrak-Toydemir, Anita Beck, Alan H. Beggs, Edward Behrens, Gill Bejerano, Jimmy Bennet, Beverly Berg-Rood, Jonathan A. Bernstein, Gerard T. Berry, Anna Bican, Stephanie Bivona, Elizabeth Blue, John Bohnsack, Carsten Bonnenmann, Devon Bonner, Lorenzo Botto, Brenna Boyd, Lauren C. Briere, Elly Brokamp, Gabrielle Brown, Elizabeth A. Burke, Lindsay C. Burrage, Manish J. Butte, Peter Byers, William E. Byrd, John Carey, Olveen Carrasquillo, Ta Chen Peter Chang, Sirisak Chanprasert, Hsiao-Tuan Chao, Gary D. Clark, Terra R. Coakley, Laurel A. Cobban, Joy D. Cogan, Matthew Coggins, F. Sessions Cole, Heather A. Colley, Cynthia M. Cooper, Heidi Cope, William J. Craigen, Andrew B. Crouse, Michael Cunningham, Precilla D’Souza, Hongzheng Dai, Surendra Dasari, Joie Davis, Jyoti G. Dayal, Matthew Deardorff, Esteban C. Dell’Angelica, Shweta U. Dhar, Katrina Dipple, Daniel Doherty, Naghmeh Dorrani, Argenia L. Doss, Emilie D. Douine, David D. Draper, Laura Duncan, Dawn Earl, David J. Eckstein, Lisa T. Emrick, Christine M. Eng, Cecilia Esteves, Marni Falk, Liliana Fernandez, Carlos Ferreira, Elizabeth L. Fieg, Laurie C. Findley, Paul G. Fisher, Brent L. Fogel, Irman Forghani, Laure Fresard, William A. Gahl, Ian Glass, Bernadette Gochuico, Rena A. Godfrey, Katie Golden-Grant, Alica M. Goldman, Madison P. Goldrich, David B. Goldstein, Alana Grajewski, Catherine A. Groden, Irma Gutierrez, Sihoun Hahn, Rizwan Hamid, Neil A. Hanchard, Kelly Hassey, Nichole Hayes, Frances High, Anne Hing, Fuki M. Hisama, Ingrid A. Holm, Jason Hom, Martha Horike-Pyne, Alden Huang, Yong Huang, Laryssa Huryn, Rosario Isasi, Fariha Jamal, Gail P. Jarvik, Jeffrey Jarvik, Suman Jayadev, Lefkothea Karaviti, Jennifer Kennedy, Dana Kiley, Isaac S. Kohane, Jennefer N. Kohler, Deborah Krakow, Donna M. Krasnewich, Elijah Kravets, Susan Korrick, Mary Koziura, Joel B. Krier, Seema R. Lalani, Byron Lam, Christina Lam, Grace L. LaMoure, Brendan C. Lanpher, Ian R. Lanza, Lea Latham, Kimberly LeBlanc, Brendan H. Lee, Hane Lee, Roy Levitt, Richard A. Lewis, Sharyn A. Lincoln, Pengfei Liu, Xue Zhong Liu, Nicola Longo, Sandra K. Loo, Joseph Loscalzo, Richard L. Maas, John MacDowall, Ellen F. Macnamara, Calum A. MacRae, Valerie V. Maduro, Marta M. Majcherska, Bryan C. Mak, May Christine V. Malicdan, Laura A. Mamounas, Teri A. Manolio, Rong Mao, Kenneth Maravilla, Thomas C. Markello, Ronit Marom, Gabor Marth, Beth A. Martin, Martin G. Martin, Julian A. Martínez-Agosto, Shruti Marwaha, Jacob McCauley, Allyn McConkie-Rosell, Colleen E. McCormack, Alexa T. McCray, Elisabeth McGee, Heather Mefford, J. Lawrence Merritt, Matthew Might, Ghayda Mirzaa, Eva Morava, Paolo Moretti, Paolo M. Moretti, Deborah Mosbrook-Davis, John J. Mulvihill, David R. Murdock, Anna Nagy, Mariko Nakano-Okuno, Avi Nath, Stan F. Nelson, John H. Newman, Sarah K. Nicholas, Deborah Nickerson, Shirley Nieves-Rodriguez, Donna Novacic, Devin Oglesbee, James P. Orengo, Laura Pace, Stephen Pak, J. Carl Pallais, Christina GS. Palmer, Jeanette C. Papp, Neil H. Parker, John A. Phillips, Jennifer E. Posey, Lorraine Potocki, Bradley Power, Barbara N. Pusey, Aaron Quinlan, Wendy Raskind, Archana N. Raja, Deepak A. Rao, Genecee Renteria, Chloe M. Reuter, Lynette Rives, Amy K. Robertson, Lance H. Rodan, Natalie Rosenwasser, Francis Rossignol, Maura Ruzhnikov, Ralph Sacco, Jacinda B. Sampson, Susan L. Samson, Mario Saporta, C. Ron Scott, Judy Schaechter, Timothy Schedl, Kelly Schoch, Daryl A. Scott, Vandana Shashi, Jimann Shin, Rebecca Signer, Edwin K. Silverman, Janet S. Sinsheimer, Kathy Sisco, Edward C. Smith, Kevin S. Smith, Emily Solem, Lilianna Solnica-Krezel, Ben Solomon, Rebecca C. Spillmann, Joan M. Stoler, Jennifer A. Sullivan, Kathleen Sullivan, Angela Sun, Shirley Sutton, David A. Sweetser, Virginia Sybert, Holly K. Tabor, Amelia L.M. Tan, Queenie K.-G. Tan, Mustafa Tekin, Fred Telischi, Willa Thorson, Audrey Thurm, Cynthia J. Tifft, Camilo Toro, Alyssa A. Tran, Brianna M. Tucker, Tiina K. Urv, Adeline Vanderver, Matt Velinder, Dave Viskochil, Tiphanie P. Vogel, Colleen E. Wahl, Stephanie Wallace, Nicole M. Walley, Chris A. Walsh, Melissa Walker, Jennifer Wambach, Jijun Wan, Lee-kai Wang, Michael F. Wangler, Patricia A. Ward, Daniel Wegner, Mark Wener, Tara Wenger, Katherine Wesseling Perry, Monte Westerfield, Matthew T. Wheeler, Jordan Whitlock, Lynne A. Wolfe, Jeremy D. Woods, Shinya Yamamoto, John Yang, Muhammad Yousef, Diane B. Zastrow, Wadih Zein, Chunli Zhao, Stephan Zuchner, Paul J. Benke, Eric S. Cameron, Vincent Strehlow, Konrad Platzer, Rami Abou Jamra, Chiara Klöckner, Matthew Osmond, Thomas Licata, Samantha Rojas, David Dyment, Josephine S.C. Chong, Sharyn Lincoln, John H. Postlethwait, Joel Krier, and Hugo J. Bellen

Subjects
0301 basic medicine, Craniofacial abnormality, Mutation, Missense, 030105 genetics & heredity, Biology, Article, Frameshift mutation, Craniofacial Abnormalities, 03 medical and health sciences, medicine, Animals, Humans, Missense mutation, Craniofacial, Allele, Zebrafish, Genetics (clinical), Loss function, Genetics, medicine.disease, biology.organism_classification, Phenotype, Spine, Growth Differentiation Factors, 030104 developmental biology, Bone Morphogenetic Proteins
Abstract

Purpose Growth differentiation factor 11 (GDF11) is a key signaling protein required for proper development of many organ systems. Only one prior study has associated an inherited GDF11 variant with a dominant human disease in a family with variable craniofacial and vertebral abnormalities. Here, we expand the phenotypic spectrum associated with GDF11 variants and document the nature of the variants. Methods We present a cohort of six probands with de novo and inherited nonsense/frameshift (4/6 patients) and missense (2/6) variants in GDF11. We generated gdf11 mutant zebrafish to model loss of gdf11 phenotypes and used an overexpression screen in Drosophila to test variant functionality. Results Patients with variants in GDF11 presented with craniofacial (5/6) , vertebral (5/6), neurological (6/6), visual (4/6), cardiac (3/6), auditory (3/6) and connective tissue abnormalities (3/6). gdf11 mutant zebrafish show craniofacial abnormalities and body segmentation defects that match some patient phenotypes. Expression of the patients’ variants in the fly showed that one nonsense variant in GDF11 is a severe loss-of-function (LOF) alleles whereas the missense variants in our cohort are partial LOF variants. Conclusion GDF11 is needed for human development, particularly neuronal development, and LOF GDF11 alleles can affect the development of numerous organs and tissues.

Published
2021
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2. Variants in PRKAR1B cause a neurodevelopmental disorder with autism spectrum disorder, apraxia, and insensitivity to pain

Author

Felix Marbach, Georgi Stoyanov, Florian Erger, Constantine A. Stratakis, Nikolaos Settas, Edra London, Jill A. Rosenfeld, Erin Torti, Chad Haldeman-Englert, Evgenia Sklirou, Elena Kessler, Sophia Ceulemans, Stanley F. Nelson, Julian A. Martinez-Agosto, Christina G.S. Palmer, Rebecca H. Signer, Maria T. Acosta, Margaret Adam, David R. Adams, Pankaj B. Agrawal, Mercedes E. Alejandro, Justin Alvey, Laura Amendola, Ashley Andrews, Euan A. Ashley, Mahshid S. Azamian, Carlos A. Bacino, Guney Bademci, Eva Baker, Ashok Balasubramanyam, Dustin Baldridge, Jim Bale, Michael Bamshad, Deborah Barbouth, Pinar Bayrak-Toydemir, Anita Beck, Alan H. Beggs, Edward Behrens, Gill Bejerano, Jimmy Bennett, Beverly Berg-Rood, Jonathan A. Bernstein, Gerard T. Berry, Anna Bican, Stephanie Bivona, Elizabeth Blue, John Bohnsack, Carsten Bonnenmann, Devon Bonner, Lorenzo Botto, Brenna Boyd, Lauren C. Briere, Elly Brokamp, Gabrielle Brown, Elizabeth A. Burke, Lindsay C. Burrage, Manish J. Butte, Peter Byers, William E. Byrd, John Carey, Olveen Carrasquillo, Ta Chen Peter Chang, Sirisak Chanprasert, Hsiao-Tuan Chao, Gary D. Clark, Terra R. Coakley, Laurel A. Cobban, Joy D. Cogan, Matthew Coggins, F. Sessions Cole, Heather A. Colley, Cynthia M. Cooper, Heidi Cope, William J. Craigen, Andrew B. Crouse, Michael Cunningham, Precilla D’Souza, Hongzheng Dai, Surendra Dasari, Joie Davis, Jyoti G. Daya, Matthew Deardorff, Esteban C. Dell’Angelica, Shweta U. Dhar, Katrina Dipple, Daniel Doherty, Naghmeh Dorrani, Argenia L. Doss, Emilie D. Douine, David D. Draper, Laura Duncan, Dawn Earl, David J. Eckstein, Lisa T. Emrick, Christine M. Eng, Cecilia Esteves, Marni Falk, Liliana Fernandez, Carlos Ferreira, Elizabeth L. Fieg, Laurie C. Findley, Paul G. Fisher, Brent L. Fogel, Irman Forghani, Laure Fresard, William A. Gahl, Ian Glass, Bernadette Gochuico, Rena A. Godfrey, Katie Golden-Grant, Alica M. Goldman, Madison P. Goldrich, David B. Goldstein, Alana Grajewski, Catherine A. Groden, Irma Gutierrez, Sihoun Hahn, Rizwan Hamid, Neil A. Hanchard, Kelly Hassey, Nichole Hayes, Frances High, Anne Hing, Fuki M. Hisama, Ingrid A. Holm, Jason Hom, Martha Horike-Pyne, Alden Huang, Yong Huang, Laryssa Huryn, Rosario Isasi, Fariha Jamal, Gail P. Jarvik, Jeffrey Jarvik, Suman Jayadev, Lefkothea Karaviti, Jennifer Kennedy, Dana Kiley, Isaac S. Kohane, Jennefer N. Kohler, Susan Korrick, Mary Kozuira, Deborah Krakow, Donna M. Krasnewich, Elijah Kravets, Joel B. Krier, Grace L. LaMoure, Seema R. Lalani, Byron Lam, Christina Lam, Brendan C. Lanpher, Ian R. Lanza, Lea Latham, Kimberly LeBlanc, Brendan H. Lee, Hane Lee, Roy Levitt, Richard A. Lewis, Sharyn A. Lincoln, Pengfei Liu, Xue Zhong Liu, Nicola Longo, Sandra K. Loo, Joseph Loscalzo, Richard L. Maas, John MacDowall, Calum A. MacRae, Ellen F. Macnamara, Valerie V. Maduro, Marta M. Majcherska, Bryan C. Mak, May Christine V. Malicdan, Laura A. Mamounas, Teri A. Manolio, Rong Mao, Kenneth Maravilla, Thomas C. Markello, Ronit Marom, Gabor Marth, Beth A. Martin, Martin G. Martin, Shruti Marwaha, Jacob McCauley, Allyn McConkie-Rosell, Colleen E. McCormack, Alexa T. McCray, Elisabeth McGee, Heather Mefford, J. Lawrence Merritt, Matthew Might, Ghayda Mirzaa, Eva Morava, Paolo M. Moretti, Paolo Moretti, Deborah Mosbrook-Davis, John J. Mulvihill, David R. Murdock, Anna Nagy, Mariko Nakano-Okuno, Avi Nath, John H. Newman, Sarah K. Nicholas, Deborah Nickerson, Shirley Nieves-Rodriguez, Donna Novacic, Devin Oglesbee, James P. Orengo, Laura Pace, Stephen Pak, J. Carl Pallais, Jeanette C. Papp, Neil H. Parker, John A. Phillips, Jennifer E. Posey, Lorraine Potocki, Bradley Power, Barbara N. Pusey, Aaron Quinlan, Archana N. Raja, Deepak A. Rao, Wendy Raskind, Genecee Renteria, Chloe M. Reuter, Lynette Rives, Amy K. Robertson, Lance H. Rodan, Natalie Rosenwasser, Francis Rossignol, Maura Ruzhnikov, Ralph Sacco, Jacinda B. Sampson, Susan L. Samson, Mario Saporta, Judy Schaechter, Timothy Schedl, Kelly Schoch, C. Ron Scott, Daryl A. Scott, Vandana Shashi, Jimann Shin, Edwin K. Silverman, Janet S. Sinsheimer, Kathy Sisco, Edward C. Smith, Kevin S. Smith, Emily Solem, Lilianna Solnica-Krezel, null Ben Solomon, Rebecca C. Spillmann, Joan M. Stoler, Jennifer A. Sullivan, Kathleen Sullivan, Angela Sun, Shirley Sutton, David A. Sweetser, Virginia Sybert, Holly K. Tabor, Amelia L.M. Tan, Queenie K.-G. Tan, Mustafa Tekin, Fred Telischi, Willa Thorson, Audrey Thurm, Cynthia J. Tifft, Camilo Toro, Alyssa A. Tran, Brianna M. Tucker, Tiina K. Urv, Adeline Vanderver, Matt Velinder, Dave Viskochil, Tiphanie P. Vogel, Colleen E. Wahl, Melissa Walker, Stephanie Wallace, Nicole M. Walley, Chris A. Walsh, Jennifer Wambach, Jijun Wan, Lee-kai Wang, Michael F. Wangler, Patricia A. Ward, Daniel Wegner, Mark Wener, Tara Wenger, Katherine Wesseling Perry, Monte Westerfield, Matthew T. Wheeler, Jordan Whitlock, Lynne A. Wolfe, Jeremy D. Woods, Shinya Yamamoto, John Yang, Muhammad Yousef, Diane B. Zastrow, Wadih Zein, Chunli Zhao, Stephan Zuchner, Marisa V. Andrews, Dorothy K. Grange, Rebecca Willaert, Richard Person, Aida Telegrafi, Aaron Sievers, Magdalena Laugsch, Susanne Theiß, YuZhu Cheng, Olivier Lichtarge, Panagiotis Katsonis, Amber Stocco, and Christian P. Schaaf

Subjects
0301 basic medicine, Apraxias, Autism Spectrum Disorder, Pain, Biology, Apraxia, Article, 03 medical and health sciences, 0302 clinical medicine, Neurodevelopmental disorder, Pregnancy, Intellectual Disability, Intellectual disability, medicine, Humans, Missense mutation, Global developmental delay, Genetics (clinical), Genetics, medicine.disease, Phenotype, Human genetics, 030104 developmental biology, Neurodevelopmental Disorders, Autism spectrum disorder, Cyclic AMP-Dependent Protein Kinase RIbeta Subunit, Female, 030217 neurology & neurosurgery
Abstract

Purpose We characterize the clinical and molecular phenotypes of six unrelated individuals with intellectual disability and autism spectrum disorder who carry heterozygous missense variants of the PRKAR1B gene, which encodes the R1β subunit of the cyclic AMP-dependent protein kinase A (PKA). Methods Variants of PRKAR1B were identified by single- or trio-exome analysis. We contacted the families and physicians of the six individuals to collect phenotypic information, performed in vitro analyses of the identified PRKAR1B-variants, and investigated PRKAR1B expression during embryonic development. Results Recent studies of large patient cohorts with neurodevelopmental disorders found significant enrichment of de novo missense variants in PRKAR1B. In our cohort, de novo origin of the PRKAR1B variants could be confirmed in five of six individuals, and four carried the same heterozygous de novo variant c.1003C>T (p.Arg335Trp; NM_001164760). Global developmental delay, autism spectrum disorder, and apraxia/dyspraxia have been reported in all six, and reduced pain sensitivity was found in three individuals carrying the c.1003C>T variant. PRKAR1B expression in the brain was demonstrated during human embryonal development. Additionally, in vitro analyses revealed altered basal PKA activity in cells transfected with variant-harboring PRKAR1B expression constructs. Conclusion Our study provides strong evidence for a PRKAR1B-related neurodevelopmental disorder.

Published
2021
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3. Commonalities across computational workflows for uncovering explanatory variants in undiagnosed cases

Author

Shilpa Nadimpalli Kobren, Dustin Baldridge, Matt Velinder, Joel B. Krier, Kimberly LeBlanc, Cecilia Esteves, Barbara N. Pusey, Stephan Züchner, Elizabeth Blue, Hane Lee, Alden Huang, Lisa Bastarache, Anna Bican, Joy Cogan, Shruti Marwaha, Anna Alkelai, David R. Murdock, Pengfei Liu, Daniel J. Wegner, Alexander J. Paul, Maria T. Acosta, Margaret Adam, David R. Adams, Pankaj B. Agrawal, Mercedes E. Alejandro, Justin Alvey, Laura Amendola, Ashley Andrews, Euan A. Ashley, Mahshid S. Azamian, Carlos A. Bacino, Guney Bademci, Eva Baker, Ashok Balasubramanyam, Jim Bale, Michael Bamshad, Deborah Barbouth, Pinar Bayrak-Toydemir, Anita Beck, Alan H. Beggs, Edward Behrens, Gill Bejerano, Jimmy Bennett, Beverly Berg-Rood, Jonathan A. Bernstein, Gerard T. Berry, Stephanie Bivona, John Bohnsack, Carsten Bonnenmann, Devon Bonner, Lorenzo Botto, Brenna Boyd, Lauren C. Briere, Elly Brokamp, Gabrielle Brown, Elizabeth A. Burke, Lindsay C. Burrage, Manish J. Butte, Peter Byers, William E. Byrd, John Carey, Olveen Carrasquillo, Ta Chen Peter Chang, Sirisak Chanprasert, Hsiao-Tuan Chao, Gary D. Clark, Terra R. Coakley, Laurel A. Cobban, Joy D. Cogan, Matthew Coggins, F. Sessions Cole, Heather A. Colley, Cynthia M. Cooper, Heidi Cope, William J. Craigen, Andrew B. Crouse, Michael Cunningham, Precilla D’Souza, Hongzheng Dai, Surendra Dasari, Joie Davis, Jyoti G. Daya, Matthew Deardorff, Esteban C. Dell’Angelica, Shweta U. Dhar, Katrina Dipple, Daniel Doherty, Naghmeh Dorrani, Argenia L. Doss, Emilie D. Douine, David D. Draper, Laura Duncan, Dawn Earl, David J. Eckstein, Lisa T. Emrick, Christine M. Eng, Marni Falk, Liliana Fernandez, Carlos Ferreira, Elizabeth L. Fieg, Laurie C. Findley, Paul G. Fisher, Brent L. Fogel, Irman Forghani, Laure Fresard, William A. Gahl, Ian Glass, Bernadette Gochuico, Rena A. Godfrey, Katie Golden-Grant, Alica M. Goldman, Madison P. Goldrich, David B. Goldstein, Alana Grajewski, Catherine A. Groden, Irma Gutierrez, Sihoun Hahn, Rizwan Hamid, Neil A. Hanchard, Kelly Hassey, Nichole Hayes, Frances High, Anne Hing, Fuki M. Hisama, Ingrid A. Holm, Jason Hom, Martha Horike-Pyne, Yong Huang, Laryssa Huryn, Rosario Isasi, Fariha Jamal, Gail P. Jarvik, Jeffrey Jarvik, Suman Jayadev, Lefkothea Karaviti, Jennifer Kennedy, Dana Kiley, Isaac S. Kohane, Jennefer N. Kohler, Susan Korrick, Mary Kozuira, Deborah Krakow, Donna M. Krasnewich, Elijah Kravets, Grace L. LaMoure, Seema R. Lalani, Byron Lam, Christina Lam, Brendan C. Lanpher, Ian R. Lanza, Lea Latham, Brendan H. Lee, Roy Levitt, Richard A. Lewis, Sharyn A. Lincoln, Xue Zhong Liu, Nicola Longo, Sandra K. Loo, Joseph Loscalzo, Richard L. Maas, John MacDowall, Calum A. MacRae, Ellen F. Macnamara, Valerie V. Maduro, Marta M. Majcherska, Bryan C. Mak, May Christine V. Malicdan, Laura A. Mamounas, Teri A. Manolio, Rong Mao, Kenneth Maravilla, Thomas C. Markello, Ronit Marom, Gabor Marth, Beth A. Martin, Martin G. Martin, Julian A. Martinez-Agosto, Jacob McCauley, Allyn McConkie-Rosell, Colleen E. McCormack, Alexa T. McCray, Elisabeth McGee, Heather Mefford, J. Lawrence Merritt, Matthew Might, Ghayda Mirzaa, Eva Morava, Paolo M. Moretti, Paolo Moretti, Deborah Mosbrook-Davis, John J. Mulvihill, Anna Nagy, Mariko Nakano-Okuno, Avi Nath, Stanley F. Nelson, John H. Newman, Sarah K. Nicholas, Deborah Nickerson, Shirley Nieves-Rodriguez, Donna Novacic, Devin Oglesbee, James P. Orengo, Laura Pace, Stephen Pak, J. Carl Pallais, Christina G.S. Palmer, Jeanette C. Papp, Neil H. Parker, John A. Phillips, Jennifer E. Posey, Lorraine Potocki, Bradley Power, Aaron Quinlan, Archana N. Raja, Deepak A. Rao, Wendy Raskind, Genecee Renteria, Chloe M. Reuter, Lynette Rives, Amy K. Robertson, Lance H. Rodan, Jill A. Rosenfeld, Natalie Rosenwasser, Francis Rossignol, Maura Ruzhnikov, Ralph Sacco, Jacinda B. Sampson, Susan L. Samson, Mario Saporta, Judy Schaechter, Timothy Schedl, Kelly Schoch, C. Ron Scott, Daryl A. Scott, Vandana Shashi, Jimann Shin, Rebecca H. Signer, Edwin K. Silverman, Janet S. Sinsheimer, Kathy Sisco, Edward C. Smith, Kevin S. Smith, Emily Solem, Lilianna Solnica-Krezel, null Ben Solomon, Rebecca C. Spillmann, Joan M. Stoler, Jennifer A. Sullivan, Kathleen Sullivan, Angela Sun, Shirley Sutton, David A. Sweetser, Virginia Sybert, Holly K. Tabor, Amelia L.M. Tan, Queenie K.-G. Tan, Mustafa Tekin, Fred Telischi, Willa Thorson, Audrey Thurm, Cynthia J. Tifft, Camilo Toro, Alyssa A. Tran, Brianna M. Tucker, Tiina K. Urv, Adeline Vanderver, Dave Viskochil, Tiphanie P. Vogel, Colleen E. Wahl, Melissa Walker, Stephanie Wallace, Nicole M. Walley, Chris A. Walsh, Jennifer Wambach, Jijun Wan, Lee-kai Wang, Michael F. Wangler, Patricia A. Ward, Daniel Wegner, Mark Wener, Tara Wenger, Katherine Wesseling Perry, Monte Westerfield, Matthew T. Wheeler, Jordan Whitlock, Lynne A. Wolfe, Jeremy D. Woods, Shinya Yamamoto, John Yang, Muhammad Yousef, Diane B. Zastrow, Wadih Zein, Chunli Zhao, Stephan Zuchner, and Shamil R. Sunyaev

Subjects
Prioritization, Genome, medicine.diagnostic_test, Genomic sequencing, Multimodal data, Computational Biology, Structural variant, Genomics, Undiagnosed Diseases, Data science, Shruti, Article, Workflow, Biomedical data, medicine, Humans, Genetic Testing, Psychology, Software, Genetics (clinical), Genetic testing
Abstract

Author(s): Kobren, Shilpa Nadimpalli; Baldridge, Dustin; Velinder, Matt; Krier, Joel B; LeBlanc, Kimberly; Esteves, Cecilia; Pusey, Barbara N; Zuchner, Stephan; Blue, Elizabeth; Lee, Hane; Huang, Alden; Bastarache, Lisa; Bican, Anna; Cogan, Joy; Marwaha, Shruti; Alkelai, Anna; Murdock, David R; Liu, Pengfei; Wegner, Daniel J; Paul, Alexander J; Undiagnosed Diseases Network; Sunyaev, Shamil R; Kohane, Isaac S | Abstract: PurposeGenomic sequencing has become an increasingly powerful and relevant tool to be leveraged for the discovery of genetic aberrations underlying rare, Mendelian conditions. Although the computational tools incorporated into diagnostic workflows for this task are continually evolving and improving, we nevertheless sought to investigate commonalities across sequencing processing workflows to reveal consensus and standard practice tools and highlight exploratory analyses where technical and theoretical method improvements would be most impactful.MethodsWe collected details regarding the computational approaches used by a genetic testing laboratory and 11 clinical research sites in the United States participating in the Undiagnosed Diseases Network via meetings with bioinformaticians, online survey forms, and analyses of internal protocols.ResultsWe found that tools for processing genomic sequencing data can be grouped into four distinct categories. Whereas well-established practices exist for initial variant calling and quality control steps, there is substantial divergence across sites in later stages for variant prioritization and multimodal data integration, demonstrating a diversity of approaches for solving the most mysterious undiagnosed cases.ConclusionThe largest differences across diagnostic workflows suggest that advances in structural variant detection, noncoding variant interpretation, and integration of additional biomedical data may be especially promising for solving chronically undiagnosed cases.

Published
2021
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4. A concurrent dual analysis of genomic data augments diagnoses: Experiences of 2 clinical sites in the Undiagnosed Diseases Network

Author

Rebecca C. Spillmann, Queenie K.-G. Tan, Chloe Reuter, Kelly Schoch, Jennefer Kohler, Devon Bonner, Diane Zastrow, Anna Alkelai, Evan Baugh, Heidi Cope, Shruti Marwaha, Matthew T. Wheeler, Jonathan A. Bernstein, Vandana Shashi, Maria T. Acosta, Margaret Adam, David R. Adams, Justin Alvey, Laura Amendola, Ashley Andrews, Euan A. Ashley, Mahshid S. Azamian, Carlos A. Bacino, Guney Bademci, Ashok Balasubramanyam, Dustin Baldridge, Jim Bale, Michael Bamshad, Deborah Barbouth, Pinar Bayrak-Toydemir, Anita Beck, Alan H. Beggs, Edward Behrens, Gill Bejerano, Hugo J. Bellen, Jimmy Bennet, Beverly Berg-Rood, Gerard T. Berry, Anna Bican, Stephanie Bivona, Elizabeth Blue, John Bohnsack, Lorenzo Botto, Brenna Boyd, Lauren C. Briere, Elly Brokamp, Gabrielle Brown, Elizabeth A. Burke, Lindsay C. Burrage, Manish J. Butte, Peter Byers, William E. Byrd, John Carey, Olveen Carrasquillo, Thomas Cassini, Ta Chen Peter Chang, Sirisak Chanprasert, Hsiao-Tuan Chao, Gary D. Clark, Terra R. Coakley, Laurel A. Cobban, Joy D. Cogan, Matthew Coggins, F. Sessions Cole, Heather A. Colley, Cynthia M. Cooper, William J. Craigen, Andrew B. Crouse, Michael Cunningham, Precilla D’Souza, Hongzheng Dai, Surendra Dasari, Joie Davis, Jyoti G. Dayal, Matthew Deardorff, Esteban C. Dell’Angelica, Katrina Dipple, Daniel Doherty, Naghmeh Dorrani, Argenia L. Doss, Emilie D. Douine, Laura Duncan, Dawn Earl, David J. Eckstein, Lisa T. Emrick, Christine M. Eng, Cecilia Esteves, Marni Falk, Liliana Fernandez, Elizabeth L. Fieg, Paul G. Fisher, Brent L. Fogel, Irman Forghani, William A. Gahl, Ian Glass, Bernadette Gochuico, Rena A. Godfrey, Katie Golden-Grant, Madison P. Goldrich, Alana Grajewski, Irma Gutierrez, Don Hadley, Sihoun Hahn, Rizwan Hamid, Kelly Hassey, Nichole Hayes, Frances High, Anne Hing, Fuki M. Hisama, Ingrid A. Holm, Jason Hom, Martha Horike-Pyne, Alden Huang, Yong Huang, Wendy Introne, Rosario Isasi, Kosuke Izumi, Fariha Jamal, Gail P. Jarvik, Jeffrey Jarvik, Suman Jayadev, Orpa Jean-Marie, Vaidehi Jobanputra, Lefkothea Karaviti, Jennifer Kennedy, Shamika Ketkar, Dana Kiley, Gonench Kilich, Shilpa N. Kobren, Isaac S. Kohane, Jennefer N. Kohler, Deborah Krakow, Donna M. Krasnewich, Elijah Kravets, Susan Korrick, Mary Koziura, Seema R. Lalani, Byron Lam, Christina Lam, Grace L. LaMoure, Brendan C. Lanpher, Ian R. Lanza, Kimberly LeBlanc, Brendan H. Lee, Roy Levitt, Richard A. Lewis, Pengfei Liu, Xue Zhong Liu, Nicola Longo, Sandra K. Loo, Joseph Loscalzo, Richard L. Maas, Ellen F. Macnamara, Calum A. MacRae, Valerie V. Maduro, Rachel Mahoney, Bryan C. Mak, May Christine V. Malicdan, Laura A. Mamounas, Teri A. Manolio, Rong Mao, Kenneth Maravilla, Ronit Marom, Gabor Marth, Beth A. Martin, Martin G. Martin, Julian A. Martínez-Agosto, Jacob McCauley, Allyn McConkie-Rosell, Alexa T. McCray, Elisabeth McGee, Heather Mefford, J. Lawrence Merritt, Matthew Might, Ghayda Mirzaa, Eva Morava, Paolo M. Moretti, Mariko Nakano-Okuno, Stan F. Nelson, John H. Newman, Sarah K. Nicholas, Deborah Nickerson, Shirley Nieves-Rodriguez, Donna Novacic, Devin Oglesbee, James P. Orengo, Laura Pace, Stephen Pak, J. Carl Pallais, Christina G.S. Palmer, Jeanette C. Papp, Neil H. Parker, John A. Phillips, Jennifer E. Posey, Lorraine Potocki, Barbara N. Pusey, Aaron Quinlan, Wendy Raskind, Archana N. Raja, Deepak A. Rao, Anna Raper, Genecee Renteria, Chloe M. Reuter, Lynette Rives, Amy K. Robertson, Lance H. Rodan, Jill A. Rosenfeld, Natalie Rosenwasser, Francis Rossignol, Maura Ruzhnikov, Ralph Sacco, Jacinda B. Sampson, Mario Saporta, Judy Schaechter, Timothy Schedl, C. Ron Scott, Daryl A. Scott, Jimann Shin, Edwin K. Silverman, Janet S. Sinsheimer, Kathy Sisco, Edward C. Smith, Kevin S. Smith, Emily Solem, Lilianna Solnica-Krezel, Ben Solomon, Joan M. Stoler, Jennifer A. Sullivan, Kathleen Sullivan, Angela Sun, Shirley Sutton, David A. Sweetser, Virginia Sybert, Holly K. Tabor, Amelia L.M. Tan, Mustafa Tekin, Fred Telischi, Willa Thorson, Cynthia J. Tifft, Camilo Toro, Alyssa A. Tran, Brianna M. Tucker, Tiina K. Urv, Adeline Vanderver, Matt Velinder, Dave Viskochil, Tiphanie P. Vogel, Colleen E. Wahl, Melissa Walker, Stephanie Wallace, Nicole M. Walley, Jennifer Wambach, Jijun Wan, Lee-kai Wang, Michael F. Wangler, Patricia A. Ward, Daniel Wegner, Monika Weisz-Hubshman, Mark Wener, Tara Wenger, Katherine Wesseling Perry, Monte Westerfield, Jordan Whitlock, Lynne A. Wolfe, Kim Worley, Changrui Xiao, Shinya Yamamoto, John Yang, Diane B. Zastrow, Zhe Zhang, Chunli Zhao, and Stephan Zuchner

Subjects
Genetics (clinical)
Published
2023
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5. One is the loneliest number: genotypic matchmaking using the electronic health record

Author

Nichole Hayes, Euan A. Ashley, Laura A. Mamounas, Allyn McConkie-Rosell, Shirley Sutton, John J.E. Mulvihill, John H. Postlethwait, Richard L. Maas, Jennefer N. Kohler, Dana Kiley, Joel B. Krier, Pankaj B. Agrawal, Xue Zhong Liu, Josh F. Peterson, Jill A. Rosenfeld, Thomas May, Jennifer E. Kyle, David A. Sweetser, Neil H. Parker, Jeanette C. Papp, Manish J. Butte, Calum A. MacRae, Rong Mao, Vandana Shashi, Christopher A. Walsh, Alica M. Goldman, Gabor T. Marth, Sharyn A. Lincoln, David Goldstein, Colleen E. McCormack, Byron L. Lam, Elly Brokamp, Lynette Rives, Lee-kai Wang, Lorraine Potocki, Mary Koziura, Matthew T. Wheeler, Teri A. Manolio, Camille L. Birch, Moretti Paolo, Willa Thorson, Fariha Jamal, Cynthia M. Cooper, Yong Huang, Matt Velinder, Catherine H. Sillari, Archana Raja, Andrea L. Gropman, J. Carl Pallais, Amy K. Robertson, Dave Viskochil, William J. Craigen, Thomas C. Markello, Devin Oglesbee, Olveen Carrasquillo, Precilla D'Souza, Lorenzo D. Botto, Hugo J. Bellen, Susan L. Samson, Jim Bale, Lisa Shakachite, Catherine Groden, Kathleen Shields, Jimann Shin, Carlos Ferreira, Lynne A. Wolfe, Melissa A. Haendel, Brent L. Fogel, Joan M. Stoler, Rebecca C. Spillmann, Roy C. Levitt, Gary D. Clark, Daniel J. Wegner, Gill Bejerano, Deborah Krakow, Ashok Balasubramanyam, J. Scott Newberry, Heidi Cope, Jijun Wan, Sandra K. Loo, Laura Duncan, Elizabeth A. Worthey, Leigh Anne Tang, Mercedes E. Alejandro, Matthew Might, Cecelia P. Tamburro, Patrick Allard, Joseph Loscalzo, Bret L. Bostwick, Lisa Emrick, Sarah K. Nicholas, David R. Murdock, Jeremy D. Woods, Alana L. Grajewski, Eva H. Baker, Lindsay C. Burrage, Stephen Pak, Camilo Toro, Ashley Andrews, James P. Orengo, Shawn Levy, Lance H. Rodan, Kelly Schoch, Jyoti G. Dayal, Thomas O. Metz, Kathy Sisco, Stephanie Bivona, Paolo Moretti, Braden E. Boone, Mahshid S. Azamian, Nicole M. Walley, Esteban C. Dell'Angelica, Rosario Isasi, Jacinda B. Sampson, F. Sessions Cole, Guoyun Yu, Rena A. Godfrey, John F. Bohnsack, Elizabeth A. Burke, John H. Newman, Alden Y. Huang, Patricia A. Ward, Barbara N. Pusey, Maria T. Acosta, Alan H. Beggs, Melissa A. Walker, Shweta U. Dhar, Edwin K. Silverman, Stephan Züchner, Ian R. Lanza, Bobbie-Jo M. Webb-Robertson, Anastasia L. Wise, Angela Jones, Nicholas Stong, Irman Forghani, Matthew H. Brush, Michael F. Wangler, Jonathan A. Bernstein, Aaron R. Quinlan, David D. Draper, Pinar Bayrak-Toydemir, Diane B. Zastrow, Daniel C. Dorset, Anna Bican, David J. Eckstein, Janet S. Sinsheimer, Isaac S. Kohane, Hsiao-Tuan Chao, May Christine V. Malicdan, C. Christopher Lau, Mariska Davids, Eva Morava-Kozicz, Beth A. Martin, Daryl A. Scott, Prashant Sharma, Elizabeth L. Fieg, Lauren C. Briere, Shinya Yamamoto, Devon Bonner, Ralph L. Sacco, Amanda J. Yoon, John Yang, Katrina M. Waters, Carlos A. Bacino, Pengfei Liu, Brendan Lee, Lisa Bastarache, Emily G. Kelley, Tiphanie P. Vogel, Jason Hom, Marta M. Majcherska, Robb Rowley, Liliana Fernandez, Carsten Bonnenmann, Stanley F. Nelson, Colleen E. Wahl, Guney Bademci, Justin Alvey, Naghmeh Dorrani, Hane Lee, Lefkothea P. Karaviti, Monte Westerfield, John A. Phillips, Laurel A. Cobban, Chunli Zhao, Nicola Longo, Donna M. Krasnewich, Ta Chen Peter Chang, Tiina K. Urv, Christine M. Eng, Chloe M. Reuter, Ingrid A. Holm, Jozef Lazar, Emilie D. Douine, Susan A. Korrick, Alexa T. McCray, Richard A. Lewis, Ronit Marom, Kimberly LeBlanc, Cynthia J. Tifft, Cecilia Esteves, David R. Adams, Donna M. Brown, Avi Nath, Rebecca Signer, Martin G. Martin, Julian A. Martinez-Agosto, Jacob L. McCauley, Alyssa A. Tran, Jennifer A. Sullivan, William A. Gahl, Brendan C. Lanpher, Marie Morimoto, Donna Novacic, Jean-Philippe F. Gourdine, Paul G. Fisher, Fred F. Telischi, Shruti Marwaha, Heather A. Colley, Queenie K.-G. Tan, Seema R. Lalani, Deborah Barbouth, Jennifer E. Posey, Yong-hui Jiang, Jennifer Wambach, Mario Saporta, Jean M. Johnston, Dustin Baldridge, Timothy Schedl, Pace Laura, Ellen Macnamara, Joy D. Cogan, Kevin S. Smith, David M. Koeller, Genecee Renteria, Maura R.Z. Ruzhnikov, Christina G.S. Palmer, Valerie Maduro, Frances A. High, Gerard T. Berry, Holly K. Tabor, Terra R. Coakley, Surendra Dasari, Neil A. Hanchard, David P. Bick, Laure Fresard, Rizwan Hamid, Lilianna Solnica-Krezel, Gabriel F. Batzli, Judy Schaechter, John C. Carey, Tyra Estwick, and Mustafa Tekin

Subjects
World Wide Web, Electronic health record, Biology, Genetics (clinical)
Published
2021
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6. Clinical sites of the Undiagnosed Diseases Network: unique contributions to genomic medicine and science

Author

Kelly Schoch, Cecilia Esteves, Anna Bican, Rebecca Spillmann, Heidi Cope, Allyn McConkie-Rosell, Nicole Walley, Liliana Fernandez, Jennefer N. Kohler, Devon Bonner, Chloe Reuter, Nicholas Stong, John J. Mulvihill, Donna Novacic, Lynne Wolfe, Ayat Abdelbaki, Camilo Toro, Cyndi Tifft, May Malicdan, William Gahl, Pengfei Liu, John Newman, David B. Goldstein, Jason Hom, Jacinda Sampson, Matthew T. Wheeler, Mercedes E. Alejandro, Mahshid S. Azamian, Carlos A. Bacino, Ashok Balasubramanyam, Lindsay C. Burrage, Hsiao-Tuan Chao, Gary D. Clark, William J. Craigen, Hongzheng Dai, Shweta U. Dhar, Lisa T. Emrick, Alica M. Goldman, Neil A. Hanchard, Fariha Jamal, Lefkothea Karaviti, Seema R. Lalani, Brendan H. Lee, Richard A. Lewis, Ronit Marom, Paolo M. Moretti, David R. Murdock, Sarah K. Nicholas, James P. Orengo, Jennifer E. Posey, Lorraine Potocki, Jill A. Rosenfeld, Susan L. Samson, Daryl A. Scott, Alyssa A. Tran, Tiphanie P. Vogel, Michael F. Wangler, Shinya Yamamoto, Christine M. Eng, Patricia A. Ward, Edward Behrens, Matthew Deardorff, Marni Falk, Kelly Hassey, Kathleen Sullivan, Adeline Vanderver, Vandana Shashi, Edward C. Smith, Rebecca C. Spillmann, Jennifer A. Sullivan, Queenie K.-G. Tan, Nicole M. Walley, Pankaj B. Agrawal, Alan H. Beggs, Gerard T. Berry, Lauren C. Briere, Laurel A. Cobban, Matthew Coggins, Cynthia M. Cooper, Elizabeth L. Fieg, Frances High, Ingrid A. Holm, Susan Korrick, Joel B. Krier, Sharyn A. Lincoln, Joseph Loscalzo, Richard L. Maas, Calum A. MacRae, J.Carl Pallais, Deepak A. Rao, Lance H. Rodan, Edwin K. Silverman, Joan M. Stoler, David A. Sweetser, Melissa Walker, Chris A. Walsh, Emily G. Kelley, Isaac S. Kohane, Kimberly LeBlanc, Alexa T. McCray, Anna Nagy, Surendra Dasari, Brendan C. Lanpher, Ian R. Lanza, Eva Morava, Devin Oglesbee, Guney Bademci, Deborah Barbouth, Stephanie Bivona, Olveen Carrasquillo, Ta Chen Peter Chang, Irman Forghani, Alana Grajewski, Rosario Isasi, Byron Lam, Roy Levitt, Xue Zhong Liu, Jacob McCauley, Ralph Sacco, Mario Saporta, Judy Schaechter, Mustafa Tekin, Fred Telischi, Willa Thorson, Stephan Zuchner, Heather A. Colley, Jyoti G. Dayal, David J. Eckstein, Laurie C. Findley, Donna M. Krasnewich, Laura A. Mamounas, Teri A. Manolio, Grace L. LaMoure, Madison P. Goldrich, Tiina K. Urv, Argenia L. Doss, Maria T. Acosta, Carsten Bonnenmann, Precilla D’Souza, David D. Draper, Carlos Ferreira, Rena A. Godfrey, Catherine A. Groden, Ellen F. Macnamara, Valerie V. Maduro, Thomas C. Markello, Avi Nath, Barbara N. Pusey, Colleen E. Wahl, Eva Baker, Elizabeth A. Burke, David R. Adams, William A. Gahl, May Christine V. Malicdan, Cynthia J. Tifft, Lynne A. Wolfe, John Yang, Bradley Power, Bernadette Gochuico, Laryssa Huryn, Lea Latham, Joie Davis, Deborah Mosbrook-Davis, Francis Rossignol, Ben Solomon, John MacDowall, Audrey Thurm, Wadih Zein, Muhammad Yousef, Margaret Adam, Laura Amendola, Michael Bamshad, Anita Beck, Jimmy Bennett, Beverly Berg-Rood, Elizabeth Blue, Brenna Boyd, Peter Byers, Sirisak Chanprasert, Michael Cunningham, Katrina Dipple, Daniel Doherty, Dawn Earl, Ian Glass, Katie Golden-Grant, Sihoun Hahn, Anne Hing, Fuki M. Hisama, Martha Horike-Pyne, Gail P. Jarvik, Jeffrey Jarvik, Suman Jayadev, Christina Lam, Kenneth Maravilla, Heather Mefford, J.Lawrence Merritt, Ghayda Mirzaa, Deborah Nickerson, Wendy Raskind, Natalie Rosenwasser, C.Ron Scott, Angela Sun, Virginia Sybert, Stephanie Wallace, Mark Wener, Tara Wenger, Euan A. Ashley, Gill Bejerano, Jonathan A. Bernstein, Terra R. Coakley, Paul G. Fisher, Laure Fresard, Yong Huang, Elijah Kravets, Marta M. Majcherska, Beth A. Martin, Shruti Marwaha, Colleen E. McCormack, Archana N. Raja, Chloe M. Reuter, Maura Ruzhnikov, Jacinda B. Sampson, Kevin S. Smith, Shirley Sutton, Holly K. Tabor, Brianna M. Tucker, Diane B. Zastrow, Chunli Zhao, William E. Byrd, Andrew B. Crouse, Matthew Might, Mariko Nakano-Okuno, Jordan Whitlock, Gabrielle Brown, Manish J. Butte, Esteban C. Dell’Angelica, Naghmeh Dorrani, Emilie D. Douine, Brent L. Fogel, Irma Gutierrez, Alden Huang, Deborah Krakow, Hane Lee, Sandra K. Loo, Bryan C. Mak, Martin G. Martin, Julian A. Martínez-Agosto, Elisabeth McGee, Stanley F. Nelson, Shirley Nieves-Rodriguez, Christina G.S. Palmer, Jeanette C. Papp, Neil H. Parker, Genecee Renteria, Rebecca H. Signer, Janet S. Sinsheimer, Jijun Wan, Lee-kai Wang, Katherine Wesseling Perry, Jeremy D. Woods, Justin Alvey, Ashley Andrews, Jim Bale, John Bohnsack, Lorenzo Botto, John Carey, Laura Pace, Nicola Longo, Gabor Marth, Paolo Moretti, Aaron Quinlan, Matt Velinder, Dave Viskochil, Pinar Bayrak-Toydemir, Rong Mao, Monte Westerfield, Elly Brokamp, Laura Duncan, Rizwan Hamid, Jennifer Kennedy, Mary Kozuira, John H. Newman, John A. Phillips, Lynette Rives, Amy K. Robertson, Emily Solem, Joy D. Cogan, F. Sessions Cole, Nichole Hayes, Dana Kiley, Kathy Sisco, Jennifer Wambach, Daniel Wegner, Dustin Baldridge, Stephen Pak, Timothy Schedl, Jimann Shin, Lilianna Solnica-Krezel, and Joy Cogan

Subjects
Exome sequencing, 0301 basic medicine, Computational biology, 030105 genetics & heredity, Genome sequencing, Article, DNA sequencing, Retrospective data, 03 medical and health sciences, Rare Diseases, Animals, Humans, Genomic medicine, Medicine, Medical diagnosis, Exome, Genetics (clinical), Retrospective Studies, Disease gene, business.industry, Genomics, 030104 developmental biology, Phenotyping, New disease, Undiagnosed diseases, Ultra-rare diseases, business
Abstract

Purpose The NIH Undiagnosed Diseases Network (UDN) evaluates participants with disorders that have defied diagnosis, applying personalized clinical and genomic evaluations and innovative research. The clinical sites of the UDN are essential to advancing the UDN mission; this study assesses their contributions relative to standard clinical practices. Methods We analyzed retrospective data from four UDN clinical sites, from July 2015 to September 2019, for diagnoses, new disease gene discoveries and the underlying investigative methods. Results Of 791 evaluated individuals, 231 received 240 diagnoses and 17 new disease-gene associations were recognized. Straightforward diagnoses on UDN exome and genome sequencing occurred in 35% (84/240). We considered these tractable in standard clinical practice, although genome sequencing is not yet widely available clinically. The majority (156/240, 65%) required additional UDN-driven investigations, including 90 diagnoses that occurred after prior nondiagnostic exome sequencing and 45 diagnoses (19%) that were nongenetic. The UDN-driven investigations included complementary/supplementary phenotyping, innovative analyses of genomic variants, and collaborative science for functional assays and animal modeling. Conclusion Investigations driven by the clinical sites identified diagnostic and research paradigms that surpass standard diagnostic processes. The new diagnoses, disease gene discoveries, and delineation of novel disorders represent a model for genomic medicine and science.

Published
2021
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7. De novo EIF2AK1 and EIF2AK2 Variants Are Associated with Developmental Delay, Leukoencephalopathy, and Neurologic Decompensation

Author

Dongxue Mao, Chloe M. Reuter, Maura R.Z. Ruzhnikov, Anita E. Beck, Emily G. Farrow, Lisa T. Emrick, Jill A. Rosenfeld, Katherine M. Mackenzie, Laurie Robak, Matthew T. Wheeler, Lindsay C. Burrage, Mahim Jain, Pengfei Liu, Daniel Calame, Sébastien Küry, Martin Sillesen, Klaus Schmitz-Abe, Davide Tonduti, Luigina Spaccini, Maria Iascone, Casie A. Genetti, Mary K. Koenig, Madeline Graf, Alyssa Tran, Mercedes Alejandro, Brendan H. Lee, Isabelle Thiffault, Pankaj B. Agrawal, Jonathan A. Bernstein, Hugo J. Bellen, Hsiao-Tuan Chao, Maria T. Acosta, Margaret Adam, David R. Adams, Mercedes E. Alejandro, Patrick Allard, Justin Alvey, Laura Amendola, Ashley Andrews, Euan A. Ashley, Mahshid S. Azamian, Carlos A. Bacino, Guney Bademci, Eva Baker, Ashok Balasubramanyam, Dustin Baldridge, Jim Bale, Michael Bamshad, Deborah Barbouth, Gabriel F. Batzli, Pinar Bayrak-Toydemir, Anita Beck, Alan H. Beggs, Gill Bejerano, Jimmy Bennet, Beverly Berg-Rood, Raphael Bernier, Gerard T. Berry, Anna Bican, Stephanie Bivona, Elizabeth Blue, John Bohnsack, Carsten Bonnenmann, Devon Bonner, Lorenzo Botto, Lauren C. Briere, Elly Brokamp, Elizabeth A. Burke, Manish J. Butte, Peter Byers, John Carey, Olveen Carrasquillo, Ta Chen Peter Chang, Sirisak Chanprasert, Gary D. Clark, Terra R. Coakley, Laurel A. Cobban, Joy D. Cogan, F. Sessions Cole, Heather A. Colley, Cynthia M. Cooper, Heidi Cope, William J. Craigen, Michael Cunningham, Precilla D’Souza, Hongzheng Dai, Surendra Dasari, Mariska Davids, Jyoti G. Dayal, Esteban C. Dell’Angelica, Shweta U. Dhar, Katrina Dipple, Daniel Doherty, Naghmeh Dorrani, Emilie D. Douine, David D. Draper, Laura Duncan, Dawn Earl, David J. Eckstein, Christine M. Eng, Cecilia Esteves, Tyra Estwick, Liliana Fernandez, Carlos Ferreira, Elizabeth L. Fieg, Paul G. Fisher, Brent L. Fogel, Irman Forghani, Laure Fresard, William A. Gahl, Ian Glass, Rena A. Godfrey, Katie Golden-Grant, Alica M. Goldman, David B. Goldstein, Alana Grajewski, Catherine A. Groden, Andrea L. Gropman, Sihoun Hahn, Rizwan Hamid, Neil A. Hanchard, Nichole Hayes, Frances High, Anne Hing, Fuki M. Hisama, Ingrid A. Holm, Jason Hom, Martha Horike-Pyne, Alden Huang, Yong Huang, Rosario Isasi, Fariha Jamal, Gail P. Jarvik, Jeffrey Jarvik, Suman Jayadev, Yong-hui Jiang, Jean M. Johnston, Lefkothea Karaviti, Emily G. Kelley, Dana Kiley, Isaac S. Kohane, Jennefer N. Kohler, Deborah Krakow, Donna M. Krasnewich, Susan Korrick, Mary Koziura, Joel B. Krier, Seema R. Lalani, Byron Lam, Christina Lam, Brendan C. Lanpher, Ian R. Lanza, C. Christopher Lau, Kimberly LeBlanc, Hane Lee, Roy Levitt, Richard A. Lewis, Sharyn A. Lincoln, Xue Zhong Liu, Nicola Longo, Sandra K. Loo, Joseph Loscalzo, Richard L. Maas, Ellen F. Macnamara, Calum A. MacRae, Valerie V. Maduro, Marta M. Majcherska, May Christine V. Malicdan, Laura A. Mamounas, Teri A. Manolio, Rong Mao, Kenneth Maravilla, Thomas C. Markello, Ronit Marom, Gabor Marth, Beth A. Martin, Martin G. Martin, Julian A. Martínez-Agosto, Shruti Marwaha, Jacob McCauley, Allyn McConkie-Rosell, Colleen E. McCormack, Alexa T. McCray, Heather Mefford, J. Lawrence Merritt, Matthew Might, Ghayda Mirzaa, Eva Morava-Kozicz, Paolo M. Moretti, Marie Morimoto, John J. Mulvihill, David R. Murdock, Avi Nath, Stan F. Nelson, John H. Newman, Sarah K. Nicholas, Deborah Nickerson, Donna Novacic, Devin Oglesbee, James P. Orengo, Laura Pace, Stephen Pak, J. Carl Pallais, Christina G.S. Palmer, Jeanette C. Papp, Neil H. Parker, John A. Phillips, Jennifer E. Posey, John H. Postlethwait, Lorraine Potocki, Barbara N. Pusey, Aaron Quinlan, Wendy Raskind, Archana N. Raja, Genecee Renteria, Lynette Rives, Amy K. Robertson, Lance H. Rodan, Robb K. Rowley, Maura Ruzhnikov, Ralph Sacco, Jacinda B. Sampson, Susan L. Samson, Mario Saporta, C. Ron Scott, Judy Schaechter, Timothy Schedl, Kelly Schoch, Daryl A. Scott, Lisa Shakachite, Prashant Sharma, Vandana Shashi, Jimann Shin, Rebecca Signer, Catherine H. Sillari, Edwin K. Silverman, Janet S. Sinsheimer, Kathy Sisco, Kevin S. Smith, Lilianna Solnica-Krezel, Rebecca C. Spillmann, Joan M. Stoler, Nicholas Stong, Jennifer A. Sullivan, Angela Sun, Shirley Sutton, David A. Sweetser, Virginia Sybert, Holly K. Tabor, Cecelia P. Tamburro, Queenie K.-G. Tan, Mustafa Tekin, Fred Telischi, Willa Thorson, Cynthia J. Tifft, Camilo Toro, Alyssa A. Tran, Tiina K. Urv, Matt Velinder, Dave Viskochil, Tiphanie P. Vogel, Colleen E. Wahl, Stephanie Wallace, Nicole M. Walley, Chris A. Walsh, Melissa Walker, Jennifer Wambach, Jijun Wan, Lee-kai Wang, Michael F. Wangler, Patricia A. Ward, Daniel Wegner, Mark Wener, Monte Westerfield, Anastasia L. Wise, Lynne A. Wolfe, Jeremy D. Woods, Shinya Yamamoto, John Yang, Amanda J. Yoon, Guoyun Yu, Diane B. Zastrow, Chunli Zhao, and Stephan Zuchner

Subjects
Male, 0301 basic medicine, Proband, Ataxia, Adolescent, Developmental Disabilities, Nervous System Malformations, Leukoencephalopathy, eIF-2 Kinase, 03 medical and health sciences, 0302 clinical medicine, Leukoencephalopathies, Report, Genetics, medicine, Humans, Missense mutation, Kinase activity, Child, Genetics (clinical), biology, Leukodystrophy, Genetic Variation, Infant, medicine.disease, White Matter, Hypotonia, Hereditary Central Nervous System Demyelinating Diseases, 030104 developmental biology, Child, Preschool, eIF2B, Immunology, biology.protein, Female, medicine.symptom, 030217 neurology & neurosurgery
Abstract

EIF2AK1 and EIF2AK2 encode members of the eukaryotic translation initiation factor 2 alpha kinase (EIF2AK) family that inhibits protein synthesis in response to physiologic stress conditions. EIF2AK2 is also involved in innate immune response and the regulation of signal transduction, apoptosis, cell proliferation, and differentiation. Despite these findings, human disorders associated with deleterious variants in EIF2AK1 and EIF2AK2 have not been reported. Here, we describe the identification of nine unrelated individuals with heterozygous de novo missense variants in EIF2AK1 (1/9) or EIF2AK2 (8/9). Features seen in these nine individuals include white matter alterations (9/9), developmental delay (9/9), impaired language (9/9), cognitive impairment (8/9), ataxia (6/9), dysarthria in probands with verbal ability (6/9), hypotonia (7/9), hypertonia (6/9), and involuntary movements (3/9). Individuals with EIF2AK2 variants also exhibit neurological regression in the setting of febrile illness or infection. We use mammalian cell lines and proband-derived fibroblasts to further confirm the pathogenicity of variants in these genes and found reduced kinase activity. EIF2AKs phosphorylate eukaryotic translation initiation factor 2 subunit 1 (EIF2S1, also known as EIF2α), which then inhibits EIF2B activity. Deleterious variants in genes encoding EIF2B proteins cause childhood ataxia with central nervous system hypomyelination/vanishing white matter (CACH/VWM), a leukodystrophy characterized by neurologic regression in the setting of febrile illness and other stressors. Our findings indicate that EIF2AK2 missense variants cause a neurodevelopmental syndrome that may share phenotypic and pathogenic mechanisms with CACH/VWM.

Published
2020
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8. Consensus interpretation of the p.Met34Thr and p.Val37Ile variants in GJB2 by the ClinGen Hearing Loss Expert Panel

Author

Kwong Wai Choy, Gema Garrido, Rebecca K. Siegert, Yoel Hirsch, Andrew R. Grant, Yu Lu, Alecia Willis, Hatice Duzkale, Lisa Schimmenti, Xue Zhong Liu, Krista Moyer, Hela Azaiez, Rebecca Mar-Heyming, Richard Smith, Narasimhan Nagan, Christine Lo, Xinhua Hu, Ahmad N. Abou Tayoun, Hyunseok Kang, Sarah E. Hemphill, Cynthia C. Morton, Yan Zhang, Yen-Fu Cheng, Huijun Yuan, Kevin T. Booth, Anne Giersch, Moshe Frydman, Tatsuo Matsunaga, Jun Shen, John H. Greinwald, Tzvi Weiden, Saurav Guha, Ye Cao, Hideki Mutai, Yukun Zeng, Arti Pandya, John J. Alexander, Lina Basel-Salmon, Marina T. DiStefano, Margaret A. Kenna, Zippora Brownstein, Ignacio del Castillo, Kejian Zhang, Bella Davidov, Sami S. Amr, Minjie Luo, Karen B. Avraham, Andrea M. Oza, Mustafa Tekin, Miguel A. Moreno-Pelayo, and Heidi L. Rehm

Subjects
ClinGen, Male, Hearing loss, Hearing Loss, Sensorineural, Population, Deafness, Compound heterozygosity, Polymorphism, Single Nucleotide, Article, Connexins, Statistical analyses, otorhinolaryngologic diseases, medicine, Humans, Allele, variant classification, Hearing Loss, education, Alleles, Genetics (clinical), Genetics, education.field_of_study, incomplete penetrance, business.industry, variant interpretation, Expert consensus, medicine.disease, Penetrance, Connexin 26, Case-Control Studies, Mutation, Female, Sensorineural hearing loss, medicine.symptom, business
Abstract

PURPOSE Pathogenic variants in GJB2 are the most common cause of autosomal recessive sensorineural hearing loss. The classification of c.101T>C/p.Met34Thr and c.109G>A/p.Val37Ile in GJB2 are controversial. Therefore, an expert consensus is required for the interpretation of these two variants. METHODS The ClinGen Hearing Loss Expert Panel collected published data and shared unpublished information from contributing laboratories and clinics regarding the two variants. Functional, computational, allelic, and segregation data were also obtained. Case-control statistical analyses were performed. RESULTS The panel reviewed the synthesized information, and classified the p.Met34Thr and p.Val37Ile variants utilizing professional variant interpretation guidelines and professional judgment. We found that p.Met34Thr and p.Val37Ile are significantly overrepresented in hearing loss patients, compared to population controls. Individuals homozygous or compound heterozygous for p.Met34Thr or p.Val37Ile typically manifest mild to moderate hearing loss. Several other types of evidence also support pathogenic roles for these two variants. CONCLUSION Resolving controversies in variant classification requires coordinated effort among a panel of international multi-institutional experts to share data, standardize classification guidelines, review evidence, and reach a consensus. We concluded that p.Met34Thr and p.Val37Ile variants in GJB2 are pathogenic for autosomal recessive nonsyndromic hearing loss with variable expressivity and incomplete penetrance.

Published
2019
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9. Magnetic Resonance Imaging characteristics in case of TOR1AIP1 muscular dystrophy

Author

Aashim Bhatia, Bret C. Mobley, Joy Cogan, Mary E. Koziura, Elly Brokamp, John Phillips, John Newman, Steven A. Moore, Rizwan Hamid, Maria T. Acosta, David R. Adams, Pankaj Agrawal, Mercedes E. Alejandro, Patrick Allard, Justin Alvey, Ashley Andrews, Euan A. Ashley, Mahshid S. Azamian, Carlos A. Bacino, Guney Bademci, Eva Baker, Ashok Balasubramanyam, Dustin Baldridge, Jim Bale, Deborah Barbouth, Gabriel F. Batzli, Pinar Bayrak-Toydemir, Alan H. Beggs, Gill Bejerano, Hugo J. Bellen, Jonathan A. Bernstein, Gerard T. Berry, Anna Bican, David P. Bick, Camille L. Birch, Stephanie Bivona, John Bohnsack, Carsten Bonnenmann, Devon Bonner, Braden E. Boone, Bret L. Bostwick, Lorenzo Botto, Lauren C. Briere, Donna M. Brown, Matthew Brush, Elizabeth A. Burke, Lindsay C. Burrage, Manish J. Butte, John Carey, Olveen Carrasquillo, Ta Chen Peter Chang, Hsiao-Tuan Chao, Gary D. Clark, Terra R. Coakley, Laurel A. Cobban, Joy D. Cogan, F. Sessions Cole, Heather A. Colley, Cynthia M. Cooper, Heidi Cope, William J. Craigen, Precilla D'Souza, Surendra Dasari, Mariska Davids, Jyoti G. Dayal, Esteban C. Dell'Angelica, Shweta U. Dhar, Naghmeh Dorrani, Daniel C. Dorset, Emilie D. Douine, David D. Draper, Laura Duncan, David J. Eckstein, Lisa T. Emrick, Christine M. Eng, Cecilia Esteves, Tyra Estwick, Liliana Fernandez, Carlos Ferreira, Elizabeth L. Fieg, Paul G. Fisher, Brent L. Fogel, Irman Forghani, Laure Fresard, William A. Gahl, Rena A. Godfrey, Alica M. Goldman, David B. Goldstein, Jean-Philippe F. Gourdine, Alana Grajewski, Catherine A. Groden, Andrea L. Gropman, Melissa Haendel, Neil A. Hanchard, Nichole Hayes, Frances High, Ingrid A. Holm, Jason Hom, Alden Huang, Yong Huang, Rosario Isasi, Fariha Jamal, Yong-hui Jiang, Jean M. Johnston, Angela L. Jones, Lefkothea Karaviti, Emily G. Kelley, Dana Kiley, David M. Koeller, Isaac S. Kohane, Jennefer N. Kohler, Deborah Krakow, Susan Korrick, Mary Koziura, Joel B. Krier, Jennifer E. Kyle, Seema R. Lalani, Byron Lam, Brendan C. Lanpher, Ian R. Lanza, C. Christopher Lau, Jozef Lazar, Kimberly LeBlanc, Brendan H. Lee, Hane Lee, Roy Levitt, Shawn E. Levy, Richard A. Lewis, Sharyn A. Lincoln, Pengfei Liu, Xue Zhong Liu, Sandra K. Loo, Richard L. Maas, Ellen F. Macnamara, Calum A. MacRae, Valerie V. Maduro, Marta M. Majcherska, May Christine V. Malicdan, Laura A. Mamounas, Teri A. Manolio, Rong Mao, Thomas C. Markello, Ronit Marom, Gabor Marth, Beth A. Martin, Martin G. Martin, Julian A. Martínez-Agosto, Shruti Marwaha, Thomas May, Jacob McCauley, Allyn McConkie-Rosell, Colleen E. McCormack, Alexa T. McCray, Thomas O. Metz, Matthew Might, Eva Morava-Kozicz, Paolo M. Moretti, Marie Morimoto, John J. Mulvihill, David R. Murdock, Avi Nath, Stan F. Nelson, J. Scott Newberry, John H. Newman, Sarah K. Nicholas, Donna Novacic, Devin Oglesbee, James P. Orengo, Laura Pace, J. Carl Pallais, Christina G.S. Palmer, Jeanette C. Papp, Neil H. Parker, John A. Phillips, Jennifer E. Posey, John H. Postlethwait, Lorraine Potocki, Barbara N. Pusey, Aaron Quinlan, Archana N. Raja, Genecee Renteria, Chloe M. Reuter, Lynette Rives, Amy K. Robertson, Lance H. Rodan, Jill A. Rosenfeld, Robb K. Rowley, Maura Ruzhnikov, Ralph Sacco, Jacinda B. Sampson, Susan L. Samson, Mario Saporta, Judy Schaechter, Timothy Schedl, Kelly Schoch, Daryl A. Scott, Lisa Shakachite, Prashant Sharma, Vandana Shashi, Kathleen Shields, Jimann Shin, Rebecca Signer, Catherine H. Sillari, Edwin K. Silverman, Janet S. Sinsheimer, Kathy Sisco, Kevin S. Smith, Lilianna Solnica-Krezel, Rebecca C. Spillmann, Joan M. Stoler, Nicholas Stong, Jennifer A. Sullivan, Shirley Sutton, David A. Sweetser, Holly K. Tabor, Cecelia P. Tamburro, Queenie K.-G. Tan, Mustafa Tekin, Fred Telischi, Willa Thorson, Cynthia J. Tifft, Camilo Toro, Alyssa A. Tran, Tiina K. Urv, Matt Velinder, Dave Viskochil, Tiphanie P. Vogel, Colleen E. Wahl, Nicole M. Walley, Chris A. Walsh, Melissa Walker, Jennifer Wambach, Jijun Wan, Lee-kai Wang, Michael F. Wangler, Patricia A. Ward, Katrina M. Waters, Bobbie-Jo M. Webb-Robertson, Daniel Wegner, Monte Westerfield, Matthew T. Wheeler, Anastasia L. Wise, Lynne A. Wolfe, Jeremy D. Woods, Elizabeth A. Worthey, Shinya Yamamoto, John Yang, Amanda J. Yoon, Guoyun Yu, Diane B. Zastrow, Chunli Zhao, and Stephan Zuchner

Subjects
medicine.medical_specialty, Adolescent, Gene mutation, Article, 030218 nuclear medicine & medical imaging, 03 medical and health sciences, 0302 clinical medicine, Atrophy, Humans, Medicine, Radiology, Nuclear Medicine and imaging, Muscular dystrophy, Muscle, Skeletal, Gluteal muscles, Muscle Weakness, Muscle biopsy, medicine.diagnostic_test, business.industry, Muscle weakness, Magnetic resonance imaging, medicine.disease, Magnetic Resonance Imaging, Muscular Atrophy, medicine.anatomical_structure, Lower Extremity, Muscular Dystrophies, Limb-Girdle, 030220 oncology & carcinogenesis, Female, Radiology, Iliopsoas, medicine.symptom, business, Molecular Chaperones
Abstract

Mutations in the torsinA-interacting protein 1 (TOR1AIP1) gene result in a severe muscular dystrophy with minimal literature in the pediatric population. We review a case of TOR1AIP1 gene mutation in a 16-year-old Caucasian female with a long history of muscle weakness. Extensive clinical workup was performed and MRI at time of initial presentation demonstrated no significant muscular atrophy with heterogenous STIR hyperintensity of the lower extremity muscles. MRI findings seven years later included extensive atrophy of the lower extremities, with severe progression, including the gluteal muscles, iliopsoas, rectus femoris, and obturator internus. There was also significant atrophy of the rectus abdominis and internal and external oblique muscles, and iliacus muscles. The MRI findings showed more proximal involvement of lower extremities and no atrophy of the tibialis anterior, making TOR1AIP1 the more likely genetic cause. Muscle biopsy findings supported TOR1AIP1 limb-girdle muscular dystrophy. Though rare, TOR1AIP1 gene mutation occurs in pediatric patients and MRI can aid in diagnosis and help differentiate from other types of muscular dystrophy. Genetic and pathology workup is also crucial to accurate diagnosis and possible treatment of these patients.

Published
2019
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10. Lysosomal Storage and Albinism Due to Effects of a De Novo CLCN7 Variant on Lysosomal Acidification

Author

Elena-Raluca Nicoli, Mary R. Weston, Mary Hackbarth, Alissa Becerril, Austin Larson, Wadih M. Zein, Peter R. Baker, John Douglas Burke, Heidi Dorward, Mariska Davids, Yan Huang, David R. Adams, Patricia M. Zerfas, Dong Chen, Thomas C. Markello, Camilo Toro, Tim Wood, Gene Elliott, Mylinh Vu, Wei Zheng, Lisa J. Garrett, Cynthia J. Tifft, William A. Gahl, Debra L. Day-Salvatore, Joseph A. Mindell, May Christine V. Malicdan, Maria T. Acosta, Pankaj Agrawal, Mercedes E. Alejandro, Patrick Allard, Justin Alvey, Ashley Andrews, Euan A. Ashley, Mahshid S. Azamian, Carlos A. Bacino, Guney Bademci, Eva Baker, Ashok Balasubramanyam, Dustin Baldridge, Jim Bale, Deborah Barbouth, Gabriel F. Batzli, Pinar Bayrak-Toydemir, Alan H. Beggs, Gill Bejerano, Hugo J. Bellen, Jonathan A. Bernstein, Gerard T. Berry, Anna Bican, David P. Bick, Camille L. Birch, Stephanie Bivona, John Bohnsack, Carsten Bonnenmann, Devon Bonner, Braden E. Boone, Bret L. Bostwick, Lorenzo Botto, Lauren C. Briere, Elly Brokamp, Donna M. Brown, Matthew Brush, Elizabeth A. Burke, Lindsay C. Burrage, Manish J. Butte, John Carey, Olveen Carrasquillo, Ta Chen Peter Chang, Hsiao-Tuan Chao, Gary D. Clark, Terra R. Coakley, Laurel A. Cobban, Joy D. Cogan, F. Sessions Cole, Heather A. Colley, Cynthia M. Cooper, Heidi Cope, William J. Craigen, Precilla D'Souza, Surendra Dasari, Jyoti G. Dayal, Esteban C. Dell'Angelica, Shweta U. Dhar, Naghmeh Dorrani, Daniel C. Dorset, Emilie D. Douine, David D. Draper, Laura Duncan, David J. Eckstein, Lisa T. Emrick, Christine M. Eng, Cecilia Esteves, Tyra Estwick, Liliana Fernandez, Carlos Ferreira, Elizabeth L. Fieg, Paul G. Fisher, Brent L. Fogel, Irman Forghani, Laure Fresard, Rena A. Godfrey, Alica M. Goldman, David B. Goldstein, Jean-Philippe F. Gourdine, Alana Grajewski, Catherine A. Groden, Andrea L. Gropman, Melissa Haendel, Rizwan Hamid, Neil A. Hanchard, Nichole Hayes, Frances High, Ingrid A. Holm, Jason Hom, Alden Huang, Yong Huang, Rosario Isasi, Fariha Jamal, Yong-hui Jiang, Jean M. Johnston, Angela L. Jones, Lefkothea Karaviti, Emily G. Kelley, Dana Kiley, David M. Koeller, Isaac S. Kohane, Jennefer N. Kohler, Deborah Krakow, Donna M. Krasnewich, Susan Korrick, Mary Koziura, Joel B. Krier, Jennifer E. Kyle, Seema R. Lalani, Byron Lam, Brendan C. Lanpher, Ian R. Lanza, C. Christopher Lau, Jozef Lazar, Kimberly LeBlanc, Brendan H. Lee, Hane Lee, Roy Levitt, Shawn E. Levy, Richard A. Lewis, Sharyn A. Lincoln, Pengfei Liu, Xue Zhong Liu, Nicola Longo, Sandra K. Loo, Joseph Loscalzo, Richard L. Maas, Ellen F. Macnamara, Calum A. MacRae, Valerie V. Maduro, Marta M. Majcherska, Laura A. Mamounas, Teri A. Manolio, Rong Mao, Ronit Marom, Gabor Marth, Beth A. Martin, Martin G. Martin, Julian A. Martínez-Agosto, Shruti Marwaha, Thomas May, Jacob McCauley, Allyn McConkie-Rosell, Colleen E. McCormack, Alexa T. McCray, Thomas O. Metz, Matthew Might, Eva Morava-Kozicz, Paolo M. Moretti, Marie Morimoto, John J. Mulvihill, David R. Murdock, Avi Nath, Stan F. Nelson, J. Scott Newberry, John H. Newman, Sarah K. Nicholas, Donna Novacic, Devin Oglesbee, James P. Orengo, Laura Pace, Stephen Pak, J. Carl Pallais, Christina G.S. Palmer, Jeanette C. Papp, Neil H. Parker, John A. Phillips, Jennifer E. Posey, John H. Postlethwait, Lorraine Potocki, Barbara N. Pusey, Aaron Quinlan, Archana N. Raja, Genecee Renteria, Chloe M. Reuter, Lynette Rives, Amy K. Robertson, Lance H. Rodan, Jill A. Rosenfeld, Robb K. Rowley, Maura Ruzhnikov, Ralph Sacco, Jacinda B. Sampson, Susan L. Samson, Mario Saporta, Judy Schaechter, Timothy Schedl, Kelly Schoch, Daryl A. Scott, Lisa Shakachite, Prashant Sharma, Vandana Shashi, Kathleen Shields, Jimann Shin, Rebecca Signer, Catherine H. Sillari, Edwin K. Silverman, Janet S. Sinsheimer, Kathy Sisco, Kevin S. Smith, Lilianna Solnica-Krezel, Rebecca C. Spillmann, Joan M. Stoler, Nicholas Stong, Jennifer A. Sullivan, Shirley Sutton, David A. Sweetser, Holly K. Tabor, Cecelia P. Tamburro, Queenie K.-G. Tan, Mustafa Tekin, Fred Telischi, Willa Thorson, Alyssa A. Tran, Tiina K. Urv, Matt Velinder, Dave Viskochil, Tiphanie P. Vogel, Colleen E. Wahl, Nicole M. Walley, Chris A. Walsh, Melissa Walker, Jennifer Wambach, Jijun Wan, Lee-kai Wang, Michael F. Wangler, Patricia A. Ward, Katrina M. Waters, Bobbie-Jo M. Webb-Robertson, Daniel Wegner, Monte Westerfield, Matthew T. Wheeler, Anastasia L. Wise, Lynne A. Wolfe, Jeremy D. Woods, Elizabeth A. Worthey, Shinya Yamamoto, John Yang, Amanda J. Yoon, Guoyun Yu, Diane B. Zastrow, Chunli Zhao, and Stephan Zuchner

Subjects
Male, 0301 basic medicine, Albinism, Antiporter, Vacuole, Article, Organomegaly, Mice, Xenopus laevis, 03 medical and health sciences, 0302 clinical medicine, Chloride Channels, Lysosome, Genetics, medicine, Lysosomal storage disease, Animals, Humans, Genetics (clinical), Hypopigmentation, biology, Chemistry, Genetic Variation, Infant, Fibroblasts, Hydrogen-Ion Concentration, medicine.disease, Molecular biology, Lysosomal Storage Diseases, 030104 developmental biology, medicine.anatomical_structure, Oocytes, biology.protein, Female, CLCN7, medicine.symptom, Lysosomes, Acids, 030217 neurology & neurosurgery, Intracellular
Abstract

Optimal lysosome function requires maintenance of an acidic pH maintained by proton pumps in combination with a counterion transporter such as the Cl(−)/H(+) exchanger, CLCN7 (ClC-7), encoded by CLCN7. The role of ClC-7 in maintaining lysosomal pH has been controversial. In this paper, we performed clinical and genetic evaluations of two children of different ethnicities. Both children had delayed myelination and development, organomegaly, and hypopigmentation, but neither had osteopetrosis. Whole-exome and -genome sequencing revealed a de novo c.2144A>G variant in CLCN7 in both affected children. This p.Tyr715Cys variant, located in the C-terminal domain of ClC-7, resulted in increased outward currents when it was heterologously expressed in Xenopus oocytes. Fibroblasts from probands displayed a lysosomal pH approximately 0.2 units lower than that of control cells, and treatment with chloroquine normalized the pH. Primary fibroblasts from both probands also exhibited markedly enlarged intracellular vacuoles; this finding was recapitulated by the overexpression of human p.Tyr715Cys CLCN7 in control fibroblasts, reflecting the dominant, gain-of-function nature of the variant. A mouse harboring the knock-in Clcn7 variant exhibited hypopigmentation, hepatomegaly resulting from abnormal storage, and enlarged vacuoles in cultured fibroblasts. Our results show that p.Tyr715Cys is a gain-of-function CLCN7 variant associated with developmental delay, organomegaly, and hypopigmentation resulting from lysosomal hyperacidity, abnormal storage, and enlarged intracellular vacuoles. Our data supports the hypothesis that the ClC-7 antiporter plays a critical role in maintaining lysosomal pH.

Published
2019
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11. Role of microRNAs in inner ear development and hearing loss

Author

Xue Zhong Liu, Denise Yan, Rahul Mittal, Sai P. Polineni, George Liu, and Nicole Bencie

Subjects
0301 basic medicine, Hearing loss, Biology, Article, 03 medical and health sciences, 0302 clinical medicine, Proper function, microRNA, otorhinolaryngologic diseases, Genetics, medicine, Animals, Humans, Auditory system, Inner ear, Hearing Loss, Cochlea, Regulation of gene expression, Hair Cells, Auditory, Inner, Regeneration (biology), General Medicine, MicroRNAs, 030104 developmental biology, medicine.anatomical_structure, Gene Expression Regulation, 030220 oncology & carcinogenesis, sense organs, medicine.symptom, Neuroscience, Signal Transduction
Abstract

The etiology of hearing loss tends to be multi-factorial and affects a significant proportion of the global population. Despite the differences in etiology, a common physical pathological change that leads to hearing loss is damage to the mechanosensory hair cells of the inner ear. MicroRNAs (miRNAs) have been shown to play a role in inner ear development and thus, may play a role in the development or prevention of hearing loss. In this paper, we review the mechanism of action of miRNAs in the auditory system. We present an overview about the role of miRNAs in inner ear development, summarize the current research on the role of miRNAs in gene regulation, and discuss the effects of both miRNA mutations as well as overexpression. We discuss the crucial role of miRNAs in ensuring normal physiological development of the inner ear. Any deviation from the proper function of miRNA in the cochlea seems to contribute to deleterious damage to the structure of the auditory system and subsequently results in hearing loss. As interest for miRNA research increases, this paper serves as a platform to review current understandings and postulate future avenues for research. A better knowledge about the role of miRNA in the auditory system will help in developing novel treatment modalities for restoring hearing function based on regeneration of damaged inner ear hair cells.

Published
2019
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12. Wnt Signaling Promotes Cell Caudalization And Inner Ear Differentiation in Mouse Stem Cell-Derived Organoids

Author

Rick F. Nelson, Li Chen, Sunita Singh, Karl R. Koehler, Xue Zhong Liu, Pei-Ciao Tang, and Andrew K. Groves

Subjects
Mouse Stem Cell, medicine.anatomical_structure, Cell, medicine, Wnt signaling pathway, Organoid, Ectoderm, Inner ear, sense organs, Biology, Otic placode, Neural plate, Cell biology
Abstract

The inner ear is derived from the otic placode, one of numerous cranial sensory placodes that emerges from the pre-placodal ectoderm (PPE). However, the molecular dynamics underlying how the PPE is induced and regionalized are poorly resolved. We used stem cell-derived inner ear organoids to investigate the effects of Wnt signaling on otic placode development and found that modulating Wnt signaling to give intermediate activation of its downstream pathway significantly increased inner ear organoid induction efficiency. Single cell RNA-sequencing revealed that the Wnt modulation induces 1) gene signatures of the posterior PPE (pPPE), 2) expansion of the caudal neural plate border (NPB), and 3) a suitable caudal head microenvironment. Our data also suggest that precursors of the pPPE committed to caudal fate during the NPB stage. Taken together, this study improves our understanding of the role of Wnt signaling in the early development of the inner ear.

Published
2021
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13. Otosclerosis

Author

Xue Zhong Liu and Thomas A. Babcock

Subjects
0301 basic medicine, Genetics, business.industry, Complex disease, General Medicine, medicine.disease, Bone remodeling, Pathogenesis, 03 medical and health sciences, 030104 developmental biology, 0302 clinical medicine, Otorhinolaryngology, medicine, Otosclerosis, 030223 otorhinolaryngology, business
Abstract

Over the past several years, with the evolution of genetic and molecular research, several etiologic factors have been implicated in the pathogenesis of otosclerosis. Overall, current evidence suggests that otosclerosis is a complex disease with a variety of potential pathways contributing to the development of abnormal bone remodeling in the otic capsule. These pathways involved in the pathogenesis of otosclerosis are influenced by both genetic and environmental factors.

Published
2018
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14. Correction: Phenotypic expansion of CACNA1C-associated disorders to include isolated neurological manifestations

Author

Lance H. Rodan, Rebecca C. Spillmann, Harley T. Kurata, Shawn M. Lamothe, Jasmine Maghera, Rami Abou Jamra, Anna Alkelai, Stylianos E. Antonarakis, Isis Atallah, Omer Bar-Yosef, Frédéric Bilan, Kathrine Bjorgo, Xavier Blanc, Patrick Van Bogaert, Yoav Bolkier, Lindsay C. Burrage, Björn U. Christ, Jorge L. Granadillo, Patricia Dickson, Kirsten A. Donald, Christèle Dubourg, Aviva Eliyahu, Lisa Emrick, Kendra Engleman, Michaela Veronika Gonfiantini, Jean-Marc Good, Judith Kalser, Chiara Kloeckner, Guus Lachmeijer, Marina Macchiaiolo, Francesco Nicita, Sylvie Odent, Emily O’Heir, Xilma Ortiz-Gonzalez, Marta Pacio-Miguez, María Palomares-Bralo, Loren Pena, Konrad Platzer, Mathieu Quinodoz, Emmanuelle Ranza, Jill A. Rosenfeld, Eliane Roulet-Perez, Avni Santani, Fernando Santos-Simarro, Ben Pode-Shakked, Cara Skraban, Rachel Slaugh, Andrea Superti-Furga, Isabelle Thiffault, Richard H. van Jaabrsveld, Marie Vincent, Hong-Gang Wang, Pia Zacher, Mercedes E. Alejandro, Mahshid S. Azamian, Carlos A. Bacino, Ashok Balasubramanyam, Hsiao-Tuan Chao, Gary D. Clark, William J. Craigen, Hongzheng Dai, Shweta U. Dhar, Lisa T. Emrick, Alica M. Goldman, Neil A. Hanchard, Fariha Jamal, Lefkothea Karaviti, Seema R. Lalani, Brendan H. Lee, Richard A. Lewis, Ronit Marom, Paolo M. Moretti, David R. Murdock, Sarah K. Nicholas, James P. Orengo, Jennifer E. Posey, Lorraine Potocki, Susan L. Samson, Daryl A. Scott, Alyssa A. Tran, Tiphanie P. Vogel, Michael F. Wangler, Shinya Yamamoto, Christine M. Eng, Pengfei Liu, Patricia A. Ward, Edward Behrens, Matthew Deardorff, Marni Falk, Kelly Hassey, Kathleen Sullivan, Adeline Vanderver, David B. Goldstein, Heidi Cope, Allyn McConkie-Rosell, Kelly Schoch, Vandana Shashi, Edward C. Smith, Jennifer A. Sullivan, Queenie K.-G. Tan, Nicole M. Walley, Pankaj B. Agrawal, Alan H. Beggs, Gerard T. Berry, Lauren C. Briere, Laurel A. Cobban, Matthew Coggins, Cynthia M. Cooper, Elizabeth L. Fieg, Frances High, Ingrid A. Holm, Susan Korrick, Joel B. Krier, Sharyn A. Lincoln, Joseph Loscalzo, Richard L. Maas, Calum A. MacRae, J. Carl Pallais, Deepak A. Rao, Edwin K. Silverman, Joan M. Stoler, David A. Sweetser, Melissa Walker, Chris A. Walsh, Cecilia Esteves, Emily G. Kelley, Isaac S. Kohane, Kimberly LeBlanc, Alexa T. McCray, Anna Nagy, Surendra Dasari, Brendan C. Lanpher, Ian R. Lanza, Eva Morava, Devin Oglesbee, Guney Bademci, Deborah Barbouth, Stephanie Bivona, Olveen Carrasquillo, Ta Chen Peter Chang, Irman Forghani, Alana Grajewski, Rosario Isasi, Byron Lam, Roy Levitt, Xue Zhong Liu, Jacob McCauley, Ralph Sacco, Mario Saporta, Judy Schaechter, Mustafa Tekin, Fred Telischi, Willa Thorson, Stephan Zuchner, Heather A. Colley, Jyoti G. Dayal, David J. Eckstein, Laurie C. Findley, Donna M. Krasnewich, Laura A. Mamounas, Teri A. Manolio, John J. Mulvihill, Grace L. LaMoure, Madison P. Goldrich, Tiina K. Urv, Argenia L. Doss, Maria T. Acosta, Carsten Bonnenmann, Precilla D’Souza, David D. Draper, Carlos Ferreira, Rena A. Godfrey, Catherine A. Groden, Ellen F. Macnamara, Valerie V. Maduro, Thomas C. Markello, Avi Nath, Donna Novacic, Barbara N. Pusey, Camilo Toro, Colleen E. Wahl, Eva Baker, Elizabeth A. Burke, David R. Adams, William A. Gahl, May Christine V. Malicdan, Cynthia J. Tifft, Lynne A. Wolfe, John Yang, Bradley Power, Bernadette Gochuico, Laryssa Huryn, Lea Latham, Joie Davis, Deborah Mosbrook-Davis, Francis Rossignol, null Ben Solomon, John MacDowall, Audrey Thurm, Wadih Zein, Muhammad Yousef, Margaret Adam, Laura Amendola, Michael Bamshad, Anita Beck, Jimmy Bennett, Beverly Berg-Rood, Elizabeth Blue, Brenna Boyd, Peter Byers, Sirisak Chanprasert, Michael Cunningham, Katrina Dipple, Daniel Doherty, Dawn Earl, Ian Glass, Katie Golden-Grant, Sihoun Hahn, Anne Hing, Fuki M. Hisama, Martha Horike-Pyne, Gail P. Jarvik, Jeffrey Jarvik, Suman Jayadev, Christina Lam, Kenneth Maravilla, Heather Mefford, J. Lawrence Merritt, Ghayda Mirzaa, Deborah Nickerson, Wendy Raskind, Natalie Rosenwasser, C. Ron Scott, Angela Sun, Virginia Sybert, Stephanie Wallace, Mark Wener, Tara Wenger, Euan A. Ashley, Gill Bejerano, Jonathan A. Bernstein, Devon Bonner, Terra R. Coakley, Liliana Fernandez, Paul G. Fisher, Laure Fresard, Jason Hom, Yong Huang, Jennefer N. Kohler, Elijah Kravets, Marta M. Majcherska, Beth A. Martin, Shruti Marwaha, Colleen E. McCormack, Archana N. Raja, Chloe M. Reuter, Maura Ruzhnikov, Jacinda B. Sampson, Kevin S. Smith, Shirley Sutton, Holly K. Tabor, Brianna M. Tucker, Matthew T. Wheeler, Diane B. Zastrow, Chunli Zhao, William E. Byrd, Andrew B. Crouse, Matthew Might, Mariko Nakano-Okuno, Jordan Whitlock, Gabrielle Brown, Manish J. Butte, Esteban C. Dell’Angelica, Naghmeh Dorrani, Emilie D. Douine, Brent L. Fogel, Irma Gutierrez, Alden Huang, Deborah Krakow, Hane Lee, Sandra K. Loo, Bryan C. Mak, Martin G. Martin, Julian A. Martínez-Agosto, Elisabeth McGee, Stanley F. Nelson, Shirley Nieves-Rodriguez, Christina G.S. Palmer, Jeanette C. Papp, Neil H. Parker, Genecee Renteria, Rebecca H. Signer, Janet S. Sinsheimer, Jijun Wan, Lee-kai Wang, Katherine Wesseling Perry, Jeremy D. Woods, Justin Alvey, Ashley Andrews, Jim Bale, John Bohnsack, Lorenzo Botto, John Carey, Laura Pace, Nicola Longo, Gabor Marth, Paolo Moretti, Aaron Quinlan, Matt Velinder, Dave Viskochil, Pinar Bayrak-Toydemir, Rong Mao, Monte Westerfield, Anna Bican, Elly Brokamp, Laura Duncan, Rizwan Hamid, Jennifer Kennedy, Mary Kozuira, John H. Newman, John A. PhillipsIII, Lynette Rives, Amy K. Robertson, Emily Solem, Joy D. Cogan, F. Sessions Cole, Nichole Hayes, Dana Kiley, Kathy Sisco, Jennifer Wambach, Daniel Wegner, Dustin Baldridge, Stephen Pak, Timothy Schedl, Jimann Shin, Lilianna Solnica-Krezel, Eric Rush, Geoffrey S. Pitt, and Ping Yee Billie Au

Subjects
Genetics (clinical)
Published
2021
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15. Characterization of UMi031-A-2 inducible pluripotent stem cell line with a neurofibromatosis type 2-associated mutation

Author

Derek M. Dykxhoorn, Aida Nourbakhsh, Xue Zhong Liu, Nicholas C. Gosstola, and Cristina Fernandez-Valle

Subjects
Pluripotent Stem Cells, Nervous system, Neurofibromatosis 2, congenital, hereditary, and neonatal diseases and abnormalities, QH301-705.5, Biology, medicine.disease_cause, law.invention, law, otorhinolaryngologic diseases, medicine, Humans, CRISPR, Biology (General), Neurofibromatosis type 2, Induced pluripotent stem cell, Neurofibromin 2, Mutation, Cell Biology, General Medicine, medicine.disease, Merlin (protein), medicine.anatomical_structure, Cancer research, Suppressor, Signal transduction, Neurilemmoma, Developmental Biology
Abstract

The UMi031-A-2 hiPSC line contains a CRISPR-induced homozygous, Neurofibromatosis Type 2 (NF2) mutation (L64P (CTG > CCG)) in the NF2 gene that encodes a merlin tumor suppressor. This line was generated from an unaffected iPSC line using CRISPR technology and characterized for pluripotency and karyotypic stability. The c.191 T > C variant in NF2 is associated with a syndromic nervous system tumor disorder leading to the development of bilateral vestibular schwannomas. Once differentiated into Schwann cells, UMi031-A-2 can serve as a resource for the analysis of signaling pathways deregulated upon merlin defects and provide a pre-clinical platform for testing therapies for NF2 schwannomas.

Published
2021
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16. Serotonin Activates Bacterial Quorum Sensing and Enhances the Virulence of Pseudomonas aeruginosa in the Host

Author

Sapna K. Deo, Pirouz Daftarian, Sylvia Daunert, Leslie D. Knecht, Gregory O'Connor, Xue Zhong Liu, and Rahul Mittal

Subjects
0301 basic medicine, Serotonin, lcsh:Medicine, Virulence, medicine.disease_cause, General Biochemistry, Genetics and Molecular Biology, Microbiology, Host-microbiome interactions, 03 medical and health sciences, chemistry.chemical_compound, 0302 clinical medicine, medicine, lcsh:R5-920, biology, Pseudomonas aeruginosa, lcsh:R, N-acyl homoserine lactone, Biofilm, Pathogenic bacteria, General Medicine, biology.organism_classification, 3. Good health, Quorum sensing, 030104 developmental biology, N-Acyl homoserine lactone, chemistry, Las pathway, Interkingdom signaling molecule, lcsh:Medicine (General), 030217 neurology & neurosurgery, Bacteria
Abstract

Bacteria in humans play an important role in health and disease. Considerable emphasis has been placed in understanding the role of bacteria in host-microbiome interkingdom communication. Here we show that serotonin, responsible for mood in the brain and motility in the gut, can also act as a bacterial signaling molecule for pathogenic bacteria. Specifically, we found that serotonin acts as an interkingdom signaling molecule via quorum sensing and that it stimulates the production of bacterial virulence factors and increases biofilm formation in vitro and in vivo in a novel mouse infection model. This discovery points out at roles of serotonin both in bacteria and humans, and at phenotypic implications not only manifested in mood behavior but also in infection processes in the host. Thus, regulating serotonin concentrations in the gut may provide with paradigm shifting therapeutic approaches.

Published
2016
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17. Recent advancements in understanding the role of epigenetics in the auditory system

Author

Susan H. Blanton, Eric Nisenbaum, Feng Gong, Christine T. Dinh, George Liu, Nicole Bencie, Denise Yan, Jeenu Mittal, Nicolas Eshraghi, Rahul Mittal, Xue Zhong Liu, and Juan I. Young

Subjects
0301 basic medicine, Hearing loss, Hearing Loss, Sensorineural, Sensory system, Deafness, Article, Epigenesis, Genetic, 03 medical and health sciences, 0302 clinical medicine, Hair Cells, Auditory, otorhinolaryngologic diseases, Genetics, medicine, Animals, Humans, Regeneration, Inner ear, Epigenetics, Hearing Loss, Zebrafish, Cochlea, Hair Cells, Auditory, Inner, biology, Regeneration (biology), Cell Differentiation, General Medicine, biology.organism_classification, 030104 developmental biology, medicine.anatomical_structure, Ear, Inner, 030220 oncology & carcinogenesis, sense organs, Hair cell, medicine.symptom, Neuroscience
Abstract

Sensorineural deafness in mammals is most commonly caused by damage to inner ear sensory epithelia, or hair cells, and can be attributed to genetic and environmental causes. After undergoing trauma, many non-mammalian organisms, including reptiles, birds, and zebrafish, are capable of regenerating damaged hair cells. Mammals, however, are not capable of regenerating damaged inner ear sensory epithelia, so that hair cell damage is permanent and can lead to hearing loss. The field of epigenetics, which is the study of various phenotypic changes caused by modification of genetic expression rather than alteration of DNA sequence, has seen numerous developments in uncovering biological mechanisms of gene expression and creating various medical treatments. However, there is a lack of information on the precise contribution of epigenetic modifications in the auditory system, specifically regarding their correlation with development of inner ear (cochlea) and consequent hearing impairment. Current studies have suggested that epigenetic modifications influence differentiation, development, and protection of auditory hair cells in cochlea, and can lead to hair cell degeneration. The objective of this article is to review the existing literature and discuss the advancements made in understanding epigenetic modifications of inner ear sensory epithelial cells. The analysis of the emerging epigenetic mechanisms related to inner ear sensory epithelial cells development, differentiation, protection, and regeneration will pave the way to develop novel therapeutic strategies for hearing loss.

Published
2020
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18. Diagnostic and therapeutic applications of genomic medicine in progressive, late-onset, nonsyndromic sensorineural hearing loss

Author

Eric Nisenbaum, George Liu, Susan H. Blanton, Denise Yan, Jason R. Rudman, Nicole Bencie, Aida Nourbakhsh, Brett Colbert, Joaquin E. Jimenez, Xue Zhong Liu, Carlos L. Green, and Rahul Mittal

Subjects
0301 basic medicine, Hearing loss, Cost-Benefit Analysis, Hearing Loss, Sensorineural, Genetic enhancement, Presbycusis, Biology, Bioinformatics, Article, Epigenesis, Genetic, 03 medical and health sciences, 0302 clinical medicine, Genome editing, Ototoxicity, Genetics, medicine, Humans, Gene Transfer Techniques, Genetic Therapy, General Medicine, medicine.disease, Clinical trial, 030104 developmental biology, 030220 oncology & carcinogenesis, Sensorineural hearing loss, medicine.symptom, Noise-induced hearing loss
Abstract

The progressive, late-onset, nonsyndromic, sensorineural hearing loss (PNSHL) is the most common cause of sensory impairment globally, with presbycusis affecting greater than a third of individuals over the age of 65. The etiology underlying PNSHL include presbycusis, noise-induced hearing loss, drug ototoxicity, and delayed-onset autosomal dominant hearing loss (AD PNSHL). The objective of this article is to discuss the potential diagnostic and therapeutic applications of genomic medicine in PNSHL. Genomic factors contribute greatly to PNSHL. The heritability of presbycusis ranges from 25 to 75%. Current therapies for PNSHL range from sound amplification to cochlear implantation (CI). PNSHL is an excellent candidate for genomic medicine approaches as it is common, has well-described pathophysiology, has a wide time window for treatment, and is amenable to local gene therapy by currently utilized procedural approaches. AD PNSHL is especially suited to genomic medicine approaches that can disrupt the expression of an aberrant protein product. Gene therapy is emerging as a potential therapeutic strategy for the treatment of PNSHL. Viral gene delivery approaches have demonstrated promising results in human clinical trials for two inherited causes of blindness and are being used for PNSHL in animal models and a human trial. Non-viral gene therapy approaches are useful in situations where a transient biologic effect is needed or for delivery of genome editing reagents (such as CRISPR/Cas9) into the inner ear. Many gene therapy modalities that have proven efficacious in animal trials have potential to delay or prevent PNSHL in humans. The development of new treatment modalities for PNSHL will lead to improved quality of life of many affected individuals and their families.

Published
2020
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19. Imaging assessment of profound sensorineural deafness with inner ear anatomical abnormalities

Author

Li Hua Tan, Zi An Xiao, Jie Qing, Peng Hu, Xin Chen, Xue Zhong Liu, Wei Jing Wu, An Quan Peng, Tao Peng, Tian Wang, Ding Hua Xie, Jing Kun Li, Yun Peng Dong, Xiang Bo He, and Shu Yang

Subjects
medicine.medical_specialty, Vestibular aqueduct, medicine.diagnostic_test, business.industry, Hearing loss, medicine.medical_treatment, Membranous labyrinth, Magnetic resonance imaging, Audiology, medicine.disease, Hypoplasia, Cochlea, medicine.anatomical_structure, Otorhinolaryngology, Multimodal imaging, Cochlear implant, otorhinolaryngologic diseases, medicine, Inner ear, sense organs, Radiology, medicine.symptom, business
Abstract

Objective To explore the value of a combined computed tomography (CT) and magnetic resonance imaging (MRI) in evaluating profound sensorineural deafness patients before cochlear implant (CI) surgery. Methods A retrospective analysis of 1012 cases of profound sensorineural deafness that received CI was performed. Results A total of 96 cases were diagnosed with inner ear abnormalities including large vestibular aqueduct syndrome (LVAS, n = 61), Michel deformity (n = 3), cochlear incomplete partition I (n = 2), cochlear incomplete partition II (n = 6), cochlear hypoplasia with vestibular malformation (n = 3), cochlear ossification (n = 3), bilateral internal auditory canal obstruction (n = 5) and internal auditory canal stenosis (n = 2). Conclusion High resolution CT (HRCT) can display bony structures while MRI can image the membranous labyrinth in preoperative evaluation for cochlear implantation. The combination of these two modalities provides reliable anatomical information regarding the bony and membranous labyrinths, as well as the auditory nerve.

Published
2015
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20. Role of innate immunity in the pathogenesis of otitis media

Author

Kalai Mathee, Jiang-Dong Li, Rahul Mittal, M'hamed Grati, Joyson Kodiyan, Robert Gerring, and Xue Zhong Liu

Subjects
Microbiology (medical), medicine.drug_class, Antibiotics, Ear, Middle, Epithelial cells, Biology, Article, lcsh:Infectious and parasitic diseases, Pathogenesis, Antibiotic resistance, medicine, Humans, Effective treatment, lcsh:RC109-216, Innate immunity, Host resistance, Innate immune system, General Medicine, Immunity, Innate, Otitis Media, Infectious Diseases, Otitis, Bacterial virulence, Mucin, Immunology, medicine.symptom
Abstract

SummaryOtitis media (OM) is a public health problem in both developed and developing countries. It is the leading cause of hearing loss and represents a significant healthcare burden. In some cases, acute OM progresses to chronic suppurative OM (CSOM), characterized by effusion and discharge, despite antimicrobial therapy. The emergence of antibiotic resistance and potential ototoxicity of antibiotics has created an urgent need to design non-conventional therapeutic strategies against OM based on modern insights into its pathophysiology. In this article, we review the role of innate immunity as it pertains to OM and discuss recent advances in understanding the role of innate immune cells in protecting the middle ear. We also discuss the mechanisms utilized by pathogens to subvert innate immunity and thereby overcome defensive responses. A better knowledge about bacterial virulence and host resistance promises to reveal novel targets to design effective treatment strategies against OM. The identification and characterization of small natural compounds that can boost innate immunity may provide new avenues for the treatment of OM. There is also a need to design novel methods for targeted delivery of these compounds into the middle ear, allowing higher therapeutic doses and minimizing systemic side effects.

Published
2014
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21. Immunity Genes and Susceptibility to Otitis Media: A Comprehensive Review

Author

Denise Yan, M'hamed Grati, Brandon Chan, Robert Gerring, Giannina Robalino, Xue Zhong Liu, and Rahul Mittal

Subjects
Male, Adolescent, Hearing loss, Chronic Suppurative Otitis Media, Disease, Biology, Family studies, Recurrence, Immunity, Genetics, medicine, Humans, Genetic Predisposition to Disease, Child, Molecular Biology, Gene, Polymorphism, Genetic, Innate immune system, Infant, Immunity, Innate, Otitis Media, Otitis, Child, Preschool, Chronic Disease, Immunology, Quality of Life, Cytokines, Female, medicine.symptom
Abstract

Otitis media (OM) is a middle ear infection associated with inflammation and pain. This disease frequently afflicts humans and is the major cause of hearing loss worldwide. OM continues to be one of the most challenging diseases in the medical field due to its diverse host targets and wide range of clinical manifestations. Substantial morbidity associated with OM is further exacerbated by high frequency of recurrent infections leading to chronic suppurative otitis media (CSOM). Children have greater susceptibility to, and thus, suffer most frequently from OM, which can cause significant deterioration in quality of life. Genetic factors have been demonstrated, in large part by twin and family studies, to be key determinants of OM susceptibility. In this review, we summarize the current knowledge on immunity genes and selected variants that have been associated with predisposition to OM. In particular, polymorphisms in innate immunity and cytokine genes have been strongly linked with the risk of developing OM. Future studies employing state-of-the-art technologies, including next-generation sequencing (NGS), will aid in the identification of novel genes associated with susceptibility to OM. This, in turn, will open up avenues for identifying high-risk individuals and designing novel therapeutic strategies based on precise targeting of these genes.

Published
2014
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22. Correction: ClinGen expert clinical validity curation of 164 hearing loss gene–disease pairs

Author

Marina T. DiStefano, Sarah E. Hemphill, Andrea M. Oza, Rebecca K. Siegert, Andrew R. Grant, Madeline Y. Hughes, Brandon J. Cushman, Hela Azaiez, Kevin T. Booth, Alex Chapin, Hatice Duzkale, Tatsuo Matsunaga, Jun Shen, Wenying Zhang, Margaret Kenna, Lisa A. Schimmenti, Mustafa Tekin, Heidi L. Rehm, Ahmad N. Abou Tayoun, Sami S. Amr, Sonia Abdelhak, John Alexander, Karen Avraham, Neha Bhatia, Donglin Bai, Nicole Boczek, Zippora Brownstein, Rachel Burt, Yasmin Bylstra, Ignacio del Castillo, Byung Yoon Choi, Lilian Downie, Thomas Friedman, Anne Giersch, Jasmine Goh, John Greinwald, Andrew J. Griffith, Amy Hernandez, Jeffrey Holt, Makoto Hosoya, Lim Jiin Ying, Kanika Jain, Un-Kyung Kim, Hannie Kremer, Ian Krantz, Suzanne Leal, Morag Lewis, Xue Zhong Liu, Wendy Low, Yu Lu, Minjie Luo, Saber Masmoudi, Tan Yuen Ming, Miguel Angel Moreno-Pelayo, Matías Morín, Cynthia Morton, Jaclyn Murray, Hideki Mutai, Kiyomitsu Nara, Arti Pandya, Sylvia Kam Pei-Rong, Richard J.H. Smith, Saumya Shekhar Jamuar, Funda Elif Suer, Shin-Ichi Usami, Guy Van Camp, Kazuki Yamazawa, Hui-Jun Yuan, Elizabeth Black-Zeigelbein, and Keijan Zhang

Subjects
medicine.medical_specialty, Text mining, business.industry, Hearing loss, Published Erratum, Clinical validity, MEDLINE, medicine, Disease, Audiology, medicine.symptom, business, Genetics (clinical)
Published
2019
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23. A Truncating Mutation in SERPINB6 Is Associated with Autosomal-Recessive Nonsyndromic Sensorineural Hearing Loss

Author

Duygu Duman, Justin Price, Xue Zhong Liu, Burcu Ozturk Hismi, Moien Kanaan, Zheng-Yi Chen, Mingqian Huang, Sevsen Kulaksizoglu, Hashem Shahin, Hilal Özdağ, Guney Bademci, Seyra Erbek, F. Basak Cengiz, Maria Grigoriadou, Mustafa Tekin, Suna Tokgoz-Yilmaz, Susan H. Blanton, Stephan Züchner, Nejat Akar, Erkan Yildirim, Asli Sirmaci, Mary Claire King, Banu Ozturk, Haris Kokotas, Michael B. Petersen, and Selçuk Üniversitesi

Subjects
Heredity, Hearing loss, Hearing Loss, Sensorineural, media_common.quotation_subject, Nonsense mutation, Nonsense, Locus (genetics), Consanguinity, Biology, 03 medical and health sciences, 0302 clinical medicine, Report, otorhinolaryngologic diseases, Genetics, medicine, Humans, Family, Genetics(clinical), Inner ear, Hearing Loss, 10. No inequality, Serpins, Genetics (clinical), Loss function, 030304 developmental biology, media_common, 0303 health sciences, Homozygote, medicine.disease, 3. Good health, medicine.anatomical_structure, Codon, Nonsense, Mutation, Sensorineural hearing loss, medicine.symptom, 030217 neurology & neurosurgery
Abstract

WOS: 000278045300016, PubMed: 20451170, More than 270 million people worldwide have hearing loss that affects normal communication. Although astonishing progress has been made in the identification of more than 50 genes for deafness during the past decade, the majority of deafness genes are yet to be identified. In this study, we mapped a previously unknown autosomal-recessive nonsyndromic sensorineural hearing loss locus (DENB91) to chromosome 6p25 in a consanguineous Turkish family. The degree of hearing loss was moderate to severe in affected individuals. We subsequently identified a nonsense mutation (p.E245X) in SERPINB6, which is located within the linkage interval for DENB91 and encodes for an intracellular protease inhibitor. The p.E245X mutation cosegregated in the family as a completely penetrant autosomal-recessive trait and was absent in 300 Turkish controls. The mRNA expression of SERPINB6 was reduced and production of protein was absent in the peripheral leukocytes of homozygotes, suggesting that the hearing loss is due to loss of function of SERPINB6. We also demonstrated that SERPINB6 was expressed primarily in the inner ear hair cells. We propose that SERPINB6 plays an important role in the inner ear in the protection against leakage of lysosomal content during stress and that loss of this protection results in cell death and sensorineural hearing loss., The Scientific AMP; Technological Research Council of Turkey [105S464, 108S045]; University of Miami; NIHUnited States Department of Health & Human ServicesNational Institutes of Health (NIH) - USA [R01 DC006908]; National Natural Science Foundation of ChinaNational Natural Science Foundation of China [30728030]; Federick and Ines Yeatts [R01 DC005575]; Oticon Fonden, Denmark, We are thankful to all participating families. We thank Professor Phillip I. Bird from Monash University, Australia, for helpful suggestions and critical reading of the manuscript. This study was partially supported by The Scientific & Technological Research Council of Turkey Grants (105S464 and 108S045), funds from the University of Miami to M.T., NIH R01 DC006908 to Z.-Y.C., National Natural Science Foundation of China to Z.-Y.C. (30728030), the Federick and Ines Yeatts inner ear hair cell regeneration fellowship to M.H., R01 DC005575 to X.Z.L., and a grant from Oticon Fonden, Denmark, to M.B.P.

Published
2010
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24. Ush1c gene expression levels in the ear and eye suggest different roles for Ush1c in neurosensory organs in a new Ush1c knockout mouse

Author

Cong Tian, Heping Yu, Denise Yan, Chantal Longo-Guess, Fengchan Han, Bin Yang, Qing Yin Zheng, Xue Zhong Liu, and Changjun Lu

Subjects
Usher syndrome, Mutant, Cell Cycle Proteins, Deafness, Biology, Blindness, Retina, Article, Mice, Genes, Reporter, Gene expression, otorhinolaryngologic diseases, medicine, Animals, Regulatory Elements, Transcriptional, RBBP7, Organ of Corti, Molecular Biology, Mice, Knockout, Genetics, Regulation of gene expression, Reporter gene, General Neuroscience, Gene Expression Regulation, Developmental, medicine.disease, Null allele, eye diseases, Cell biology, Cytoskeletal Proteins, Disease Models, Animal, Phenotype, Lac Operon, Ear, Inner, Knockout mouse, sense organs, Neurology (clinical), Carrier Proteins, Usher Syndromes, Photoreceptor Cells, Vertebrate, Developmental Biology
Abstract

Usher syndrome (USH) is the most common form of deaf-blindness in humans. Molecular characterization revealed that the USH gene products form a macromolecular protein network in hair cells of the inner ear and in photoreceptor cells of the retina via binding to PDZ domains in the scaffold protein harmonin encoded by the Ush1c gene in mice and humans. Although several mouse mutants for the Ush1c gene have been described, we generated a targeted null mutation Ush1c mouse model in which the first four exons of the Ush1c gene were replaced with a reporter gene. Here, we assessed the expression pattern of the reporter gene under control of Ush1c regulatory elements and characterized the phenotype of mice defective for Ush1c. These Ush1 knockout mice are deaf but do not recapitulate vision defects before 10 months of age. Our data show LacZ expression in multiple layers of the retina but in neither outer nor inner segments of the photoreceptor layers in mice bearing the knockout construct at 1–5 months of age. The fact that Ush1c expression is much higher in the ear than in the eye suggests a different role for Ush1c in ear function than in the eye and may explain why Ush1c mutant mice do not recapitulate vision defects.

Published
2010
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25. Two new molybdenum(V) phosphates containing sandwich-shaped clusters with zero- and three-dimensional structures

Author

Bizhou Lin, Bai-Huan Xu, Qin-Qin Wang, Xue-Zhong Liu, and Zi-Jing Xiao

Subjects
chemistry.chemical_element, General Chemistry, Crystal structure, Condensed Matter Physics, Hydrothermal circulation, Rhodamine, Crystallography, chemistry.chemical_compound, Metallate, chemistry, Molybdenum, Hydrothermal synthesis, General Materials Science, Cyclic voltammetry, Group 2 organometallic chemistry
Abstract

Two reduced molybdenum(V) phosphates, (H2dien)4[CaMo12O24(OH)6(HPO4)8]·nH2O (1) and (H2dien)4[Ba2(H2O)4CaMo12O24(OH)6(HPO4)4(PO4)4]·nH2O (2) (dien = diethylenetriamine) have been prepared under hydrothermal conditions and characterized by elemental analyses, IR, UV–vis, cyclic voltammetry and single-crystal X-ray diffraction. [Mo6P4] units in both structures are linked by octahedrally coordinated Ca(II) cations into sandwich-shaped [Ca(Mo6P4)2] clusters. While the clusters in 1 are discrete, those in 2 are interconnected through BaO9 polyhedra into a three-dimensional framework structure. It was indicated that the compounds exhibit photocatalytic activity in the bleaching of rhodamine B.

Published
2008
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26. Cochlear implantation in individuals with Usher type 1 syndrome

Author

Denise Yan, Kaukab Rajput, Thomas J. Balkany, Annelle V. Hodges, Fred F. Telischi, Simon I. Angeli, Adrien A. Eshraghi, and Xue Zhong Liu

Subjects
medicine.medical_specialty, Usher syndrome, medicine.medical_treatment, DNA Mutational Analysis, education.educational_degree, Cadherin Related Proteins, Cell Cycle Proteins, Deafness, Myosins, Audiology, Gene mutation, Habilitation, Cochlear implant, otorhinolaryngologic diseases, medicine, Humans, Child, education, Polymorphism, Single-Stranded Conformational, Adaptor Proteins, Signal Transducing, medicine.diagnostic_test, Genetic heterogeneity, business.industry, Age Factors, Dyneins, Auditory Threshold, General Medicine, Cadherins, medicine.disease, Cochlear Implantation, Cytoskeletal Proteins, Otorhinolaryngology, Child, Preschool, Myosin VIIa, Mutation, Pediatrics, Perinatology and Child Health, Speech Perception, Pure tone audiometry, business, Usher Syndromes, PCDH15, Case series
Abstract

Summary Objective To analyze the occurrence of the Usher type 1 (USH1) gene mutations in cochlear implant recipients with deaf-blind Usher syndrome, and to assess the potential effect of these genes and other factors on the therapeutic outcome. Study design Case series study of nine patients with the phenotypic diagnosis of USH1. Methods and subjects Mutation analysis of four USH1 genes (MYO7A, USH1C, CDH23, and PCDH15) by single strand conformational polymorphism (SSCP) and direct sequencing methods. Pre- and post-implantation audiologic tests including pure tone audiometry, speech perception measures, and qualitative assessment of auditory performance. Nine USH1 patients who received their cochlear implants at the University of Miami Ear Institute, Miami, FL, USA, and at the Department of Cochlear Implants, Great Ormond Street Hospital for Children, London, UK. Results DNA samples from five of the nine patients were available for mutation analysis. Three of the five patients were found to carry USH1 mutations including two with a truncated mutation in CDH23 and one being a digenic inheritance with mutations in CDH23 and PCDH15. We may have failed to detect mutations in the amplicons analyzed, as neither SSCP nor direct sequencing, even combined, detects all mutations present. Our failure to detect mutations in all five patients may also confirm the genetic heterogeneity of USH1 and additional USH1 loci remain to be mapped. Pre-implantation assessment indicated that all of the subjects were pre-linguistically profoundly deaf, had no consistent response to sound, had varying degrees of auditory-oral habilitation. Age at implantation ranged from 2 to 11 years. There was post-implantation improvement in sound detection and speech recognition measures in closed-set format in all patients. Children implanted at an age of 3 years or less showed good open-set speech perception with lip-reading. All patients are implant users. Those patients who do not show open-set perception still use the cochlear implant as an adjunct of lip-reading or total communication. Conclusion Testing for mutations in the USH1 genes allows early identification and intervention of children with USH1; timely intervention is important to maximize the development of useful auditory-oral communication skills prior to the onset of the visual impairment.

Published
2008
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27. Synthesis and characterization of new two-dimensional molybdenum(V) phosphates: (Hen)6[M2(H2O)Mo12O24(OH)6(H2PO4)3(HPO4)4(PO4)]·4H2O (M =K, Na)

Author

Yi-Lin Chen, Bizhou Lin, Xue-Zhong Liu, Xiu-Feng Huang, and Liwen He

Subjects
Chemistry, Hydrogen bond, Organic Chemistry, Supramolecular chemistry, chemistry.chemical_element, Ethylenediamine, Crystal structure, Analytical Chemistry, Inorganic Chemistry, Rhodamine, chemistry.chemical_compound, Crystallography, Molybdenum, Hydrothermal synthesis, Molecule, Spectroscopy
Abstract

Two new reduced molybdenum(V) phosphates, (Hen)6[K2(H2O)Mo12O24(OH)6(H2PO4)3(HPO4)4(PO4)]·4H2O and (Hen)6[Na2(H2O)Mo12O24(OH)6(H2PO4)3(HPO4)4(PO4)]·4H2O (en = ethylenediamine) have been prepared under hydrothermal conditions and characterized by elemental analyses, IR and single-crystal X-ray diffraction. It was revealed that the sandwich-shaped units [M(Mo6P4)2] are linked by additional octahedrally-coordinated K or Na atoms into two-dimensional layers. The ethylenediamine cations and the lattice water molecules are nestled in the spaces between layers, and are interacted with the inorganic networks through hydrogen bonds into a three-dimensional supramolecular framework. It was indicated that the compounds exhibit photocatalytic activity in the degradation of rhodamine B.

Published
2008
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28. A novel layer formed by paradodecatungstate clusters and {Cu(en)2}2+ bridging groups: Synthesis and characterization of [{Cu(en)2}4(H4W12O42)]·9H2O

Author

Xue-Zhong Liu, Xiu-Feng Huang, Liwen He, Bizhou Lin, and Yun-Long Feng

Subjects
Materials science, Maleic anhydride, Nanotechnology, General Chemistry, Crystal structure, Condensed Matter Physics, Catalysis, chemistry.chemical_compound, Crystallography, Metallate, chemistry, Hydrothermal synthesis, General Materials Science, Cyclic voltammetry, Single crystal, Group 2 organometallic chemistry
Abstract

A novel two-dimensional solid, [{Cu(en)2}4(H4W12O42)]·9H2O (en = ethylenediamine), has been prepared under mild hydrothermal conditions. Single crystal X-ray diffraction revealed that each paradodecatungstate [H4W12O42]8− cluster in the title compound is connected with its four adjacent clusters through eight {Cu(en)2}2+ bridging groups into a two-dimensional layered structure. Its cyclic voltammetric behavior in aqueous electrolyte demonstrated that its modified carbon paste electrode has a good stability. A probe reaction indicated that the catalytic activity of paradodecatungstates in epoxidation of maleic anhydride has been enhanced by assembling paradodecatungstate clusters into extended structures.

Published
2008
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29. Preparation and characterization of organic–inorganic poly(ethylene glycol)/WS2 nanocomposite

Author

Xue-Zhong Liu, Zi-Jing Xiao, Bai-Huan Xu, Dong-Ya Sun, Bizhou Lin, and Cong Ding

Subjects
Nanocomposite, Materials science, Mechanical Engineering, Tungsten disulfide, Intercalation (chemistry), Condensed Matter Physics, Oligomer, chemistry.chemical_compound, Chemical engineering, chemistry, Mechanics of Materials, PEG ratio, Organic chemistry, General Materials Science, Thermal stability, Thermal analysis, Ethylene glycol
Abstract

Layered nanocomposite PEG/WS2, intercalating oligomeric poly(ethylene glycol) (PEG6000) into the tungsten disulfide host galleries, was synthesized using the exfoliation-adsorption technique. X-ray diffraction revealed that the intercalated oligomer within the host galleries is in a double-layer arrangement with an interlayer expansion of about 8.8 A. The optimum conditions were explored to prepare the single-phase product with a composition of Li0.12(PEG)1.51WS2. Thermal analyses suggested that the resulting material shows good thermal stability, with the decomposition of the interacted oligomeric chains within the disulfide galleries occurring at around 258 °C. Despite high conductivity of the host material, those of the PEG/WS2 nanocomposite were found to be high in the order of 1 × 10−2 S cm−1 at ambient temperature, resulted from the host guest–host charge transfers.

Published
2007
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30. First Strandberg-type polyoxotungstate compound: Synthesis and characterization of organic–inorganic hybrid (H2en)(Hen)2[H2P2W5O23]·5.42H2O

Author

Cong Ding, Zhen Li, Bai-Huan Xu, Xue-Zhong Liu, Liwen He, and Bi-Zhou Lin

Subjects
Thermogravimetric analysis, Organic Chemistry, Supramolecular chemistry, chemistry.chemical_element, Crystal structure, Tungsten, Ring (chemistry), Analytical Chemistry, Inorganic Chemistry, Crystallography, Octahedron, chemistry, Cyclic voltammetry, Single crystal, Spectroscopy
Abstract

The first Strandberg-type polyoxotungstate compound, (H 2 en)(Hen) 2 [H 2 P 2 W 5 O 23 ]·5.42H 2 O (en = ethylenediamine), has been hydrothermally synthesized and characterized by single crystal X-ray diffraction, elemental analyses, IR, UV–vis spectra, thermogravimetric analyses and cyclic voltammetry measurements. It was revealed that the Strandberg-type polyoxotungstate cluster can be considered as a ring formed by five distorted edge- and corner-sharing WO 6 octahedra, capped on both poles by a phosphate tetrahedron sharing three vertices with the ring tungsten centers. The Strandberg clusters are connected with the organic amines through hydrogen-bonding interactions into a three-dimensional supramolecular network.

Published
2006
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31. Corrigendum to 'Serotonin Activates Bacterial Quorum Sensing and Enhances the Virulence of Pseudomonas aeruginosa in the Host' [EBioMedicine 9 (2016) 161–169]

Author

Rahul Mittal, Sylvia Daunert, Sapna K. Deo, Gregory O'Connor, Pirouz Daftarian, Patrizia Pasini, Leslie D. Knecht, and Xue Zhong Liu

Subjects
Serotonin, lcsh:Medicine, Virulence, Biology, medicine.disease_cause, General Biochemistry, Genetics and Molecular Biology, Microbiology, Host-microbiome interactions, Mice, Bacterial Proteins, Pregnancy, Malondialdehyde, medicine, Animals, Intestinal Mucosa, Peroxidase, lcsh:R5-920, Host (biology), Pseudomonas aeruginosa, lcsh:R, N-acyl homoserine lactone, General Medicine, Catalase, Intestines, Mice, Inbred C57BL, Quorum sensing, Phenotype, Microscopy, Electron, Scanning, Cytokines, Female, Las pathway, lcsh:Medicine (General), Corrigendum, Interkingdom signaling molecule, Injections, Intraperitoneal, Peptide Hydrolases, Research Paper
Abstract

Bacteria in humans play an important role in health and disease. Considerable emphasis has been placed in understanding the role of bacteria in host-microbiome interkingdom communication. Here we show that serotonin, responsible for mood in the brain and motility in the gut, can also act as a bacterial signaling molecule for pathogenic bacteria. Specifically, we found that serotonin acts as an interkingdom signaling molecule via quorum sensing and that it stimulates the production of bacterial virulence factors and increases biofilm formation in vitro and in vivo in a novel mouse infection model. This discovery points out at roles of serotonin both in bacteria and humans, and at phenotypic implications not only manifested in mood behavior but also in infection processes in the host. Thus, regulating serotonin concentrations in the gut may provide with paradigm shifting therapeutic approaches., Highlights • Serotonin can act as a bacterial quorum sensing molecule through the LasR quorum sensing pathway. • Serotonin stimulates quorum sensing-dependent virulence factor and biofilm production in Pseudomonas aeruginosa. • Serotonin exacerbates Pseudomonas aeruginosa infection in vivo. Bacteria play many roles in human health and disease, thus investigating host-microbiome communication is of great importance. To this end, our research demonstrates that serotonin, a neurotransmitter responsible for mood in the brain and motility in the gut, can act as a bacterial communication molecule for pathogenic bacteria, specifically Pseudomonas aeruginosa. Serotonin increases Pseudomonas virulence factor and biofilm production in vitro and enhances virulence in infected mice. These findings are beneficial in understanding the impact of the microbiome on human health and may open the door for novel treatments for human disease.

Published
2017
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32. A Mutation (2314delG) in the Usher Syndrome Type IIA Gene: High Prevalence and Phenotypic Variation

Author

Trevor Cole, Karen P. Steel, Sarah Bundey, Jiu Mu Zou, Walter E. Nance, Carolyn Hope, Steve D.M. Brown, Chuan Yu Liang, Robert F. Mueller, Li Rong Xu, and Xue-Zhong Liu

Subjects
Adult, Male, China, medicine.medical_specialty, Letter, Adolescent, genetic structures, European community, Usher syndrome, education, Deafness, Biology, Phenotypic variation, Retinitis pigmentosa, Prevalence, otorhinolaryngologic diseases, Genetics, medicine, Humans, Genetics(clinical), Age of Onset, Child, USH2A gene, Atypical Usher syndrome, health care economics and organizations, Genetics (clinical), Sequence Deletion, Extracellular Matrix Proteins, High prevalence, Genetic Variation, Infant, Syndrome, Middle Aged, medicine.disease, United Kingdom, eye diseases, Child, Preschool, Family medicine, Mutation, Mutation (genetic algorithm), Female, Retinitis Pigmentosa
Abstract

This work was supported by the Medical Research Council, by Defeating Deafness of the United Kingdom, by European Community grant CT96-1324, and by National Institutes of Health R01 grant DC02530. C.H. acknowledges support from the British Retinitis Pigmentosa Society and The Birmingham Eye Foundation.

Published
1999
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33. Mutations in the Myosin VIIA Gene Cause a Wide Phenotypic Spectrum, Including Atypical Usher Syndrome

Author

Jiu Mu Zhou, Chuan Yu Liang, Dorothy Trump, Karen P. Steel, James Walsh, Xiao Mei Ke, Sarah Bundey, Xue-Zhong Liu, Steve D.M. Brown, Carolyn Hope, Li Ron Xu, and Valerie Newton

Subjects
Genetics, Mutation, Myosin VIIa, genetic structures, MYO7A, Usher syndrome, education, Usher Syndrome Type 1, Biology, medicine.disease, medicine.disease_cause, Medical research, eye diseases, Phenotypic spectrum, Myosin VIIA, Retinitis pigmentosa, otorhinolaryngologic diseases, medicine, Genetics(clinical), Gene, Atypical Usher syndrome, health care economics and organizations, Genetics (clinical), Mutation scanning
Abstract

This work was supported by the Medical Research Council (U.K.), Defeating Deafness—the Hearing Research Trust, and SENSE and by European Community grant CT96-1324. C.H. acknowledges support from the British Retinitis Pigmentosa Society and the Birmingham Eye Foundation.

Published
1998
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34. Corrigendum to 'Zearalenone impairs the male reproductive system functions via inducing structural and functional alterations of sertoli cells' [Environ. Toxicol. Pharmacol. 42 (2016) 146–155]

Author

Qing Liu, Guangguang Wang, Xue Zhong Liu, Jian Chun Bian, Yan Yuan, Ya Jun Wang, Wanglong Zheng, Jianhong Gu, Zong Ping Liu, and ShunYe Pan

Subjects
Pharmacology, medicine.medical_specialty, Health, Toxicology and Mutagenesis, General Medicine, Biology, Toxicology, Sertoli cell, chemistry.chemical_compound, Endocrinology, medicine.anatomical_structure, chemistry, Internal medicine, medicine, Male reproductive system, Zearalenone
Published
2016
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35. Characterization of a Unique Myosin IIIa Deafness Mutation which Enhances Actin-Sliding Velocity but Abolishes Filopodia Tip Localization

Author

Xue Zhong Liu, Lina Jamis, Manmeet H. Raval, M'hamed Grati, Omar A. Quintero, Jasmine Crenshaw, Christopher M. Yengo, and William C. Unrath

Subjects
Mutation, Stereocilia (inner ear), Biophysics, Motility, macromolecular substances, Myosin IIIA, Biology, medicine.disease_cause, Cell biology, Myosin, medicine, Filopodia, Cellular localization, Actin
Abstract

MYO3A, an unconventional myosin that localizes to the distal tips of stereocilia in the sensory epithelia of the vertebrate auditory and vestibular systems, consists of an N-terminal kinase domain, an actin-activated motor domain, and a class-specific tail domain. Previous work indicates that MYO3A tip-localization is regulated through autophosphorylation. MYO3A is thought to transport the actin regulatory protein, ESPIN1, to the stereocilia tips in inner ear hair cells and mutations in MYO3A lead to non-syndromic deafness in humans. We investigated the G488E mutation in MYO3A, a deafness associated mutation located near the conserved switch I region. The G488E mutation reduces the maximum actin-activated ATPase rate 2-fold and increases 10-fold the actin concentration required to reach one-half maximal ATPase. Interestingly, G488E MYO3A increases 2-fold the actin filament sliding velocity measured with the in vitro motility assay. We also investigated the impact of the G488E mutation on cellular localization by examining GFP tagged MYO3A dK constructs transfected into COS7 cells. The G488E mutation completely abolished MYO3A dK filopodia tip localization both in the presence and absence of ESPIN1. In addition, co-transfection of G488E MYO3A dK, ESPIN1 and wild-type (WT) MYO3A dK demonstrated that the presence of WT MYO3A does not rescue the tip localization of G488E. We hypothesize that the G488E mutation disrupts the duty ratio which prevents processive movement to the tips of parallel actin bundles. In support, chimeras of the MYO3A tail with other myosin motors (MYO1A, MYO19, MYO5A, and MYO10) demonstrate that only high duty-ratio motors are capable of filopodia tip localization. Our results demonstrate that intra-filopodia motility requires high duty ratio motor activity, which may be crucial for the formation, maintenance, and ultrastructure of parallel actin bundles.

Published
2016
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36. WITHDRAWN: Hepatoprotective effects of Achyranthes bidentata polysaccharides on dimethoate-induced oxidative stress, and histopathological and ultrastructural changes in liver of rats

Author

Jin-Gui Li, Xue-Zhong Liu, and Kai Yuan

Subjects
chemistry.chemical_classification, biology, Health, Toxicology and Mutagenesis, General Medicine, Pharmacology, Polysaccharide, biology.organism_classification, medicine.disease_cause, Toxicology, chemistry.chemical_compound, chemistry, medicine, Ultrastructure, Agronomy and Crop Science, Dimethoate, Achyranthes bidentata, Oxidative stress
Published
2009
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38. Relation between choice of partner and high frequency of connexin-26 deafness

Author

Walter E. Nance, Arti Pandya, and Xue Zhong Liu

Subjects
Genetics, Mutation, Genotype, Hearing loss, Connexin, Genes, Recessive, General Medicine, Deafness, Biology, medicine.disease_cause, Connexins, Genetic determinism, Connexin 26, Phenotype, otorhinolaryngologic diseases, medicine, Humans, medicine.symptom
Abstract

Recessive mutations at the connexin-26 gene locus are now recognised as the cause of nearly half of all cases of genetic deafness in many populations. We suggest that this high frequency is only seen in populations with a long tradition of intermarriage among deaf people. Available data are consistent with the hypothesis that such marriages might well have contributed to the high frequency of connexin-26 deafness in the USA, and could represent a novel mechanism for maintaining specific genotypes at unexpectedly high frequencies.

Published
2000
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39. Connexin-26 deafness in the United States: Are we ready for the next Millennium?

Author

K S Amos, R Morrell, S H Blanton, Walter E. Nance, Thomas B. Friedman, J R Albertorio, Xue Zhong Liu, K. Oelrich, Arti Pandya, and Xia Juan Xia

Subjects
Proband, Genetics, education.field_of_study, Hearing loss, business.industry, Nonsense mutation, Population, Locus (genetics), Compound heterozygosity, otorhinolaryngologic diseases, medicine, Allele, medicine.symptom, education, business, Gene, Genetics (clinical)
Abstract

Profound hearing loss has an incidence of 1:1000 children, and is genetically determined in at least half of the cases. The GJB2 gene encoding the gap junction protein 2, also called Connexin 26, is one of a growing number of genes found to have mutations which can result in hearing loss. One particular GJB2 mutation, 35delG accounts for 50-80% of recessive deafness in the Caucasian population of European descent. A second mutation, 167delT has a high prevalence in the Ashkenazi Jewish population with a carrier frequency of about 4%. At least 40 other GJB2 alleles associated with hearing loss have been reported. There is significant phenotypic variability both in the severity and progression of hearing impairment. This, coupled with the relative ease of testing for mutations at this locus, has raised important ethical and social issues when counseling deaf probands and their families. To address these issues and to obtain more accurate estimates of the frequency of different mutations at the GJB2 locus in the US population, we ascertained deaf probands from both multiplex and simplex families through a national survey conducted by the Research Institute at Gallaudet University, as well as from the student body at Gallaudet University. Molecular analysis was performed by direct fluorescent sequencing of the coding region of the GJB2 locus. So far, we have observed five previously described and two new mutations. An Arg32Cys substitution at a highly conserved residue in the first transmembrane domain was observed in a compound heterozygote with congenital deafness. We also found a novel nonsense mutation at codon 136 in a compound heterozygote. Connexin deafness accounted for 24% of the 92 US probands, and 79% of the mutant alleles were 35delG. Analysis of audiometric data on more than half of these probands is presented with comparison to previous studies. Identification of the mutational spectrum at this locus will allow a careful genotype-phenotype correlation and provide more accurate estimates of the frequencies of various GJB2 alleles. This will enable provision of accurate diagnosis, prognosis and counseling for appropriate language and speech development as well as for future recurrence risk.

Published
2000
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40. Is Assortative Mating the Cause for the High Frequency of Connexin 26 (Cx 26) Deafness?

Author

Walter E. Nance, Xue Zhong Liu, and Arti Pandya

Subjects
Genetics, Proband, education.field_of_study, Offspring, media_common.quotation_subject, Population, Assortative mating, Connexin, Fertility, Biology, otorhinolaryngologic diseases, Mating, education, Allele frequency, Genetics (clinical), media_common
Abstract

Recessive mutations at Cx 26 are known to be the cause of nearly half of all genetic deafness in many populations. Since assortative mating is known to increase the variance of continuous traits and the frequency of qualitative genetic phenotypes (such as recessive deafness), it seems possible that the high frequency of Cx 26 deafness may be related to the mating structure of the deaf population. During the past 200 years, improvements in educational, social and economic circumstances have lead to an increase in the fertility of the deaf along with the appearance of assortative mating in many western populations including the United States. The new deaf by deaf mating pool has increased the frequency of common forms of recessive deafness such as Cx 26 because the non-complementary matings which produce many of the deaf offspring from these marriages are proportional to the fourth power of the gene frequency. Existing data on the frequency of non-complementary marriages among the deaf in the 19th century suggest that the incidence of Cx 26 deafness has increased in the past 100 years along with the proportion of deaf children bom to deaf parents. Current observations also suggest that the high frequency of Cx 26 deafness may be confined to populations with a long tradition of intermarriage among the deaf. In Japan, for example, Fuse et al (Neuro report 10:1853, 1999) found Cx 26 deafness in only four of 20 multiplex sibships (20%). The comparable rate for multiplex probands in the U.S. is 49% (Green et al, JAMA 281:2211, 1999). Although we are not aware of data on the frequency of deaf by deaf matings in Japan, they were virtually unheard of in India in the past, and accounted for only about 1% of the marriages of the deaf in a reported survey from China (Liu et al, Chinese Med Genet 5:193, 1988). All of these findings are consistent with the hypothesis that variation in the mating structure may have contributed to differences in the current distribution of this trait throughout the world.

Published
2000
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