@article {800, title = {Multi-omic studies on missense PLG variants in families with otitis media.}, journal = {Sci Rep}, volume = {10}, year = {2020}, month = {2020 09 14}, pages = {15035}, abstract = {

Otitis media (OM), a very common disease in young children, can result in hearing loss. In order to potentially replicate previously reported associations between OM and PLG, exome and Sanger sequencing, RNA-sequencing of saliva and middle ear samples, 16S rRNA sequencing, molecular modeling, and statistical analyses including transmission disequilibrium tests (TDT) were performed in a multi-ethnic cohort of 718 families and simplex cases with OM. We identified four rare PLG variants c.112A > G (p.Lys38Glu), c.782G > A (p.Arg261His), c.1481C > T (p.Ala494Val) and c.2045~T > A (p.Ile682Asn), and one common variant c.1414G > A (p.Asp472Asn). However TDT analyses for these PLG variants did not demonstrate association with OM in 314 families. Additionally PLG expression is very low or absent in normal or diseased middle ear in mouse and human, and salivary expression and microbial α-diversity were non-significant in c.1414G > A (p.Asp472Asn) carriers. Based on molecular modeling, the novel rare variants particularly c.782G > A (p.Arg261His) and c.2045~T > A (p.Ile682Asn) were predicted to affect protein structure. Exploration of other potential disease mechanisms will help elucidate how PLG contributes to OM susceptibility in humans. Our results underline the importance of following up findings from genome-wide association through replication studies, preferably using multi-omic datasets.

}, keywords = {Animals, Ear, Middle, Female, Genomics, Humans, Male, Mice, Microbiota, Mutation, Missense, Otitis Media, Pedigree, Plasminogen, Polymorphism, Single Nucleotide, Saliva}, issn = {2045-2322}, doi = {10.1038/s41598-020-70498-w}, author = {Bootpetch, Tori C and Hafr{\'e}n, Lena and Elling, Christina L and Baschal, Erin E and Manichaikul, Ani W and Pine, Harold S and Szeremeta, Wasyl and Scholes, Melissa A and Cass, Stephen P and Larson, Eric D and Chan, Kenny H and Ishaq, Rafaqat and Prager, Jeremy D and Shaikh, Rehan S and Gubbels, Samuel P and Yousaf, Ayesha and Wine, Todd M and Bamshad, Michael J and Yoon, Patricia J and Jenkins, Herman A and Nickerson, Deborah A and Streubel, Sven-Olrik and Friedman, Norman R and Frank, Daniel N and Einarsdottir, Elisabet and Kere, Juha and Riazuddin, Saima and Daly, Kathleen A and Leal, Suzanne M and Ryan, Allen F and Mattila, Petri S and Ahmed, Zubair M and Sale, Michele M and Chonmaitree, Tasnee and Santos-Cortez, Regie Lyn P} } @article {699, title = {A2ML1 and otitis media: novel variants, differential expression, and relevant pathways.}, journal = {Hum Mutat}, volume = {40}, year = {2019}, month = {2019 08}, pages = {1156-1171}, abstract = {

A genetic basis for otitis media is established, however, the role of rare variants in disease etiology is largely unknown. Previously a duplication variant within A2ML1 was identified as a significant risk factor for otitis media in an indigenous Filipino population and in US children. In this report exome and Sanger sequencing was performed using DNA samples from the indigenous Filipino population, Filipino cochlear implantees, US probands, Finnish, and Pakistani families with otitis media. Sixteen novel, damaging A2ML1 variants identified in otitis media patients were rare or low-frequency in population-matched controls. In the indigenous population, both gingivitis and A2ML1 variants including the known duplication variant and the novel splice variant c.4061 + 1 G>C were independently associated with otitis media. Sequencing of salivary RNA samples from indigenous Filipinos demonstrated lower A2ML1 expression according to the carriage of A2ML1 variants. Sequencing of additional salivary RNA samples from US patients with otitis media revealed differentially expressed genes that are highly correlated with A2ML1 expression levels. In particular,~RND3 is upregulated in both A2ML1 variant carriers and high-A2ML1 expressors. These findings support a role for A2ML1 in keratinocyte differentiation within the middle ear as part of otitis media pathology and the potential application of ROCK inhibition in otitis media.

}, issn = {1098-1004}, doi = {10.1002/humu.23769}, author = {Larson, Eric D and Magno, Jose Pedrito M and Steritz, Matthew J and Llanes, Erasmo Gonzalo D V and Cardwell, Jonathan and Pedro, Melquiadesa and Roberts, Tori Bootpetch and Einarsdottir, Elisabet and Rosanes, Rose Anne Q and Greenlee, Christopher and Santos, Rachel Ann P and Yousaf, Ayesha and Streubel, Sven-Olrik and Santos, Aileen Trinidad R and Ruiz, Amanda G and Lagrana-Villagracia, Sheryl Mae and Ray, Dylan and Yarza, Talitha Karisse L and Scholes, Melissa A and Anderson, Catherine B and Acharya, Anushree and Gubbels, Samuel P and Bamshad, Michael J and Cass, Stephen P and Lee, Nanette R and Shaikh, Rehan S and Nickerson, Deborah A and Mohlke, Karen L and Prager, Jeremy D and Cruz, Teresa Luisa G and Yoon, Patricia J and Abes, Generoso T and Schwartz, David A and Chan, Abner L and Wine, Todd M and Cutiongco-de la Paz, Eva Maria and Friedman, Norman and Kechris, Katerina and Kere, Juha and Leal, Suzanne M and Yang, Ivana V and Patel, Janak A and Tantoco, Ma Leah C and Riazuddin, Saima and Chan, Kenny H and Mattila, Petri S and Reyes-Quintos, Maria Rina T and Ahmed, Zubair M and Jenkins, Herman A and Chonmaitree, Tasnee and Hafr{\'e}n, Lena and Chiong, Charlotte M and Santos-Cortez, Regie Lyn P} } @article {661, title = {FUT2 Variants Confer Susceptibility to Familial Otitis Media.}, journal = {Am J Hum Genet}, volume = {103}, year = {2018}, month = {2018 11 01}, pages = {679-690}, abstract = {

Non-secretor status due to homozygosity for the common FUT2 variant c.461G>A (p.Trp154) is associated with either risk for autoimmune diseases or protection against viral diarrhea and HIV. We determined the role of FUT2 in otitis media susceptibility by obtaining DNA samples from 609 multi-ethnic families and simplex case subjects with otitis media. Exome and Sanger sequencing, linkage analysis, and Fisher exact and transmission disequilibrium tests (TDT) were performed. The common FUT2 c.604C>T (p.Arg202) variant co-segregates with otitis media in a Filipino pedigree (LOD = 4.0). Additionally, a rare variant, c.412C>T (p.Arg138Cys), is associated with recurrent/chronic otitis media in European-American children (p = 1.2~{\texttimes} 10) and US trios (TDT p = 0.01). The c.461G>A (p.Trp154) variant was also over-transmitted in US trios (TDT p = 0.01) and was associated with shifts in middle ear microbiota composition (PERMANOVA p < 10) and increased biodiversity. When all missense and nonsense variants identified in multi-ethnic US trios with CADD > 20 were combined, FUT2 variants were over-transmitted in trios (TDT p = 0.001). Fut2 is transiently upregulated in mouse middle ear after inoculation with non-typeable Haemophilus influenzae. Four FUT2 variants-namely p.Ala104Val, p.Arg138Cys, p.Trp154, and p.Arg202-reduced A antigen in mutant-transfected COS-7 cells, while the nonsense variants also reduced FUT2 protein levels. Common and rare FUT2 variants confer susceptibility to otitis media, likely by modifying the middle ear microbiome through regulation of A antigen levels in epithelial cells. Our families demonstrate marked intra-familial genetic heterogeneity, suggesting that multiple combinations of common and rare variants plus environmental factors influence the individual otitis media phenotype as a complex trait.

}, issn = {1537-6605}, doi = {10.1016/j.ajhg.2018.09.010}, author = {Santos-Cortez, Regie Lyn P and Chiong, Charlotte M and Frank, Daniel N and Ryan, Allen F and Giese, Arnaud P J and Bootpetch Roberts, Tori and Daly, Kathleen A and Steritz, Matthew J and Szeremeta, Wasyl and Pedro, Melquiadesa and Pine, Harold and Yarza, Talitha Karisse L and Scholes, Melissa A and Llanes, Erasmo Gonzalo D V and Yousaf, Saira and Friedman, Norman and Tantoco, Ma Leah C and Wine, Todd M and Labra, Patrick John and Benoit, Jeanne and Ruiz, Amanda G and de la Cruz, Rhodieleen Anne R and Greenlee, Christopher and Yousaf, Ayesha and Cardwell, Jonathan and Nonato, Rachelle Marie A and Ray, Dylan and Ong, Kimberly Mae C and So, Edward and Robertson, Charles E and Dinwiddie, Jordyn and Lagrana-Villagracia, Sheryl Mae and Gubbels, Samuel P and Shaikh, Rehan S and Cass, Stephen P and Einarsdottir, Elisabet and Lee, Nanette R and Schwartz, David A and Gloria-Cruz, Teresa Luisa I and Bamshad, Michael J and Yang, Ivana V and Kere, Juha and Abes, Generoso T and Prager, Jeremy D and Riazuddin, Saima and Chan, Abner L and Yoon, Patricia J and Nickerson, Deborah A and Cutiongco-de la Paz, Eva Maria and Streubel, Sven-Olrik and Reyes-Quintos, Maria Rina T and Jenkins, Herman A and Mattila, Petri and Chan, Kenny H and Mohlke, Karen L and Leal, Suzanne M and Hafr{\'e}n, Lena and Chonmaitree, Tasnee and Sale, Michele M and Ahmed, Zubair M} } @article {403, title = {Molecular outcomes, clinical consequences, and genetic diagnosis of Oculocutaneous Albinism in Pakistani population.}, journal = {Sci Rep}, volume = {7}, year = {2017}, month = {2017 03 07}, pages = {44185}, abstract = {

Nonsyndromic oculocutaneous Albinism (nsOCA) is clinically characterized by the loss of pigmentation in the skin, hair, and iris. OCA is amongst the most common causes of vision impairment in children. To date, pathogenic variants in six genes have been identified in individuals with nsOCA. Here, we determined the identities, frequencies, and clinical consequences of OCA alleles in 94 previously unreported Pakistani families. Combination of Sanger and Exome sequencing revealed 38 alleles, including 22 novel variants, segregating with nsOCA phenotype in 80 families. Variants of TYR and OCA2 genes were the most common cause of nsOCA, occurring in 43 and 30 families, respectively. Twenty-two novel variants include nine missense, four splice site, two non-sense, one insertion and six gross deletions. In vitro studies revealed retention of OCA proteins harboring novel missense alleles in the endoplasmic reticulum (ER) of transfected cells. Exon-trapping assays with constructs containing splice site alleles revealed errors in splicing. As eight alleles account for approximately 56\% (95\% CI: 46.52-65.24\%) of nsOCA cases, primarily enrolled from Punjab province of Pakistan, hierarchical strategies for variant detection would be feasible and cost-efficient genetic tests for OCA in families with similar origin. Thus, we developed Tetra-primer ARMS assays for rapid, reliable, reproducible and economical screening of most of these common alleles.

}, keywords = {Albinism, Oculocutaneous, Alleles, Female, Gene Frequency, Humans, Male, Membrane Transport Proteins, Mutation, Missense, Pakistan}, issn = {2045-2322}, doi = {10.1038/srep44185}, author = {Shahzad, Mohsin and Yousaf, Sairah and Waryah, Yar M and Gul, Hadia and Kausar, Tasleem and Tariq, Nabeela and Mahmood, Umair and Ali, Muhammad and Khan, Muzammil A and Waryah, Ali M and Shaikh, Rehan S and Riazuddin, Saima and Ahmed, Zubair M} } @article {117, title = {Identification and clinical characterization of Hermansky-Pudlak syndrome alleles in the Pakistani population.}, journal = {Pigment Cell Melanoma Res}, volume = {29}, year = {2016}, month = {2016 Mar}, pages = {231-5}, keywords = {Adolescent, Adult, Alleles, Child, Child, Preschool, Female, Hermanski-Pudlak Syndrome, Humans, Infant, Male, Membrane Proteins, Middle Aged, Pakistan, Pedigree}, issn = {1755-148X}, doi = {10.1111/pcmr.12438}, author = {Yousaf, Sairah and Shahzad, Mohsin and Kausar, Tasleem and Sheikh, Shakeel A and Tariq, Nabeela and Shabbir, Asra S and Ali, Muhammad and Waryah, Ali M and Shaikh, Rehan S and Riazuddin, Saima and Ahmed, Zubair M} } @article {142, title = {Identification and functional characterization of natural human melanocortin 1 receptor mutant alleles in Pakistani population.}, journal = {Pigment Cell Melanoma Res}, volume = {28}, year = {2015}, month = {2015 Nov}, pages = {730-5}, abstract = {

Melanocortin 1 receptor (MC1R), a Gs protein-coupled receptor of the melanocyte{\textquoteright}s plasma membrane, is a major determinant of skin pigmentation and phototype. Upon activation by α-melanocyte stimulating hormone, MC1R triggers the cAMP cascade to stimulate eumelanogenesis. We used whole-exome sequencing to identify causative alleles in Pakistani families with skin and hair hypopigmentation. Six MC1R mutations segregated with the phenotype in seven families, including a p.Val174del in-frame deletion and a p.Tyr298* nonsense mutation, that were analyzed for function in heterologous HEK293 cells. p.Tyr298* MC1R showed no agonist-induced signaling to the cAMP or ERK pathways, nor detectable agonist binding. Conversely, signaling was comparable for p.Val174del and wild-type in HEK cells overexpressing the proteins, but binding analysis suggested impaired cell surface expression. Flow cytometry and confocal imaging studies revealed reduced plasma membrane expression of p.Val174del and p.Tyr298*. Therefore, p.Tyr298* was a total loss-of-function (LOF) allele, while p.Val174del displayed a partial LOF attribute.

}, keywords = {Alleles, Family, Female, Humans, Hypopigmentation, Male, Mutation, Pakistan, Pedigree, Phenotype, Receptor, Melanocortin, Type 1}, issn = {1755-148X}, doi = {10.1111/pcmr.12400}, author = {Shahzad, Mohsin and Sires Campos, Julia and Tariq, Nabeela and Herraiz Serrano, Cecilia and Yousaf, Rizwan and Jim{\'e}nez-Cervantes, Celia and Yousaf, Sairah and Waryah, Yar M and Dad, Haseeb A and Blue, Elizabeth M and Sobreira, Nara and L{\'o}pez-Gir{\'a}ldez, Francesc and Kausar, Tasleem and Ali, Muhammad and Waryah, Ali M and Riazuddin, Saima and Shaikh, Rehan S and Garc{\'\i}a-Borr{\'o}n, Jos{\'e} C and Ahmed, Zubair M} }