Research Project: Enhancing Genetic Resistance to Marek’s Disease in Poultry

Location: Endemic Poultry Viral Diseases Research

Publications (Clicking on the reprint icon will take you to the publication reprint.)

An atlas of regulatory elements in chicken: A resource for chicken genetics and genomics - (Peer Reviewed Journal)
Pan, Z., Wang, Y., Wang, M., Wang, Z., Zhu, X., Gu, S., Zhong, C., An, L., Damas, J., Halsted, M., Cheng, H.H., Zhou, H. 2023. An atlas of regulatory elements in chicken: A resource for chicken genetics and genomics. Science Advances. 9:eade1204. https://www.science.org/doi/10.1126/sciadv.ade1204.

The immune cell landscape and response of Marek's disease resistant and susceptible chickens infected with Marek's disease virus - (Peer Reviewed Journal)
Warren, W.C., Rice, E.S., Meyer, A., Hearn, C.J., Steep, A., Hunt, H.D., Monson, M.S., Lamont, S.J., Cheng, H.H. 2023. The immune cell landscape and response of Marek's disease resistant and susceptible chickens infected with Marek's disease virus. Scientific Reports. 13. Article 5355. https://doi.org/10.1038/s41598-023-32308-x.

Role of T cells in vaccine-mediated immunity against Marek’s Disease - (Peer Reviewed Journal)
Heidari, M., Zhang, H., Sunkara, L.T., Ahmad, S. 2023. Role of T cells in vaccine-mediated immunity against Marek’s Disease. Viruses. 15. Article 648. https://doi.org/10.3390/v15030648.

Small RNA deep sequencing revealed microRNAs’ involvement in modulating cellular senescence and immortalization state - (Peer Reviewed Journal)
Zhu, C., Zhang, L., Heidari, M., Sun, S., Chang, S., Qingmei, X., Ai, Y., Dong, K., Zhang, H. 2023. Small RNA deep sequencing revealed microRNAs’ involvement in modulating cellular senescence and immortalization state. Poultry Science. 102(3):102474. https://doi.org/10.1016/j.psj.2022.102474.

Prediction of transcript isoforms in 19 chicken tissues by Oxford Nanopore long-read sequencing - (Peer Reviewed Journal)
Guan, D., Halsted, M.M., Islas-Trejo, A.D., Goszczynski, D.E., Cheng, H.H., Ross, P.J., Zhou, H. 2022. Prediction of transcript isoforms in 19 chicken tissues by Oxford Nanopore long-read sequencing. Frontiers in Genetics. 13:997460. https://doi.org/10.3389/fgene.2022.997460.

A comprehensive analysis of avian lymphoid leukosis-like lymphoma transcriptomes including identification of LncRNAs and the expression profiles - (Peer Reviewed Journal)
Dong, K., Heidari, M., Mays, J.K., Chang, S., Xie, Q., Zhang, L., Ai, Y., Zhang, H. 2022. A comprehensive analysis of avian lymphoid leukosis-like lymphoma transcriptomes including identification of LncRNAs and the expression profiles. PLOS ONE. 17(8):e0272557. https://doi.org/10.1371/journal.pone.0272557.

Comparative RNA-Seq analysis reveals insights in Salmonella disease resistance of chicken; and database development as resource for gene expression in poultry - (Peer Reviewed Journal)
Dar, M.A., Ahmad, S.M., Bhat, B.A., Dar, T.A., Ul Haq, Z., Wani, B.A., Shabir, N., Kashoo, Z.A., Ganai, N.A., Heidari, M., Shah, R.A. 2022. Comparative RNA-Seq analysis reveals insights in Salmonella disease resistance of chicken; and database development as resource for gene expression in poultry. Genomics. 114(5):110475. https://doi.org/10.1016/j.ygeno.2022.110475.

MDV-induced differential microRNA expression in the primary lymphoid organ of thymus - (Peer Reviewed Journal)
Heidari, M., Zhang, H., Sunkara, L. 2022. MDV-induced differential microRNA expression in the primary lymphoid organ of thymus. Microbial Pathogenesis. 170. Article 105688. https://doi.org/10.1016/j.micpath.2022.105688.

The emergence, diversification, and transmission of Subgroup J Avian Leukosis Virus reveals that the live chicken trade plays a critical role in the adaption and endemicity of viruses to the yellow-chickens - (Peer Reviewed Journal)
Deng, Q., Li, Q., Li, M., Zhang, S., Wang, P., Fu, F., Zhu, W., Wei, T., Mo, M., Huang, T., Zhang, H., Wei, P. 2022. The emergence, diversification, and transmission of Subgroup J Avian Leukosis Virus reveals that the live chicken trade plays a critical role in the adaption and endemicity of viruses to the yellow-chickens. Journal of Virology. 96(17):e0071722. https://doi.org/10.1128/jvi.00717-22.

ALV-miRNA-p19-01 promotes viral replication via targeting dual specificity Phosphatase 6 - (Peer Reviewed Journal)
Yan, Y., Chen, S., Liao, S., Gao, S., Pang, Y., Zhang, X., Zhang, H., Xie, Q. 2022. ALV-miRNA-p19-01 promotes viral replication via targeting dual specificity Phosphatase 6. Viruses. https://doi.org/10.3390/v14040805.

Transcriptome-wide dynamics of m6A methylation in tumor livers induced by ALV-J infection in chickens - (Peer Reviewed Journal)
Zhang, X., Zhao, Q., Yao, Z., Chen, L., He, Y., Xie, Z., Zhang, H., Lin, W., Chen, F., Xie, Q. 2022. Transcriptome-wide dynamics of m6A methylation in tumor livers induced by ALV-J infection in chickens. Journal of Immunology. 13. Article 868892. https://doi.org/10.3389/fimmu.2022.868892.

Identification and validation of Ikaros (IKZF1) as a cancer driver gene for Marek’s disease virus-induced lymphomas - (Peer Reviewed Journal)
Steep, A., Hildebrandt, E.C., Xu, H., Hearn, C.J., Frishman, D., Niikura, M., Dunn, J.R., Kim, T.N., Conrad, S.J., Muir, W.M., Cheng, H.H. 2022. Identification and validation of Ikaros (IKZF1) as a cancer driver gene for Marek’s disease virus-induced lymphomas. Microorganisms. 10(2):401. https://doi.org/10.3390/microorganisms10020401.

Semen Exosomes Mediate Vertical Transmission of Subgroup J Avian Leukosis Virus - (Peer Reviewed Journal)
Liao, L., Chen, W., Zhang, X., Zhang, H., Li, A., Yan, Y., Zhang, X., Li, H., Lin, W., Ma, J., Xie, Q. 2022. Semen Exosomes Mediate Vertical Transmission of Subgroup J Avian Leukosis Virus. Journal of Virology. https://doi.org/10.1016/j.virs.2022.01.026.

B cells do not play a role in vaccine-mediated immunity against Marek's disease - (Peer Reviewed Journal)
Heidari, M., Zhang, H., Hearn, C.J., Sunkara, L. 2021. B cells do not play a role in vaccine-mediated immunity against Marek's disease. Vaccine. 10:100128. https://doi.org/10.1016/j.jvacx.2021.100128.

Darwinian genomics and diversity in the tree of life - (Peer Reviewed Journal)
Stephan, T., Burgess, S.M., Cheng, H.H., Danko, C., Gill, C.A., Jarvis, E.D., Koepfli, K., Koltes, J.E., Lyons, E., Ronald, P., Ryder, O.A., Schriml, L.M., Soltis, P., Vandewoude, S., Zhou, H., Ostrander, E.A., Karlsson, E.K. 2022. Darwinian genomics and diversity in the tree of life. Proceedings of the National Academy of Sciences(PNAS). 119:4. https://doi.org/10.1073/pnas.2115644119.

Anti-CD81 antibodies block vertical transmission of avian leukosis virus subgroup J - (Peer Reviewed Journal)
Liao, L., Wu, Z., Chen, W., Zhang, H., Li, A., Yan, Y., Xie, Z., Li, H., Lin, W., Ma, J., Zhang, X., Xie, Q. 2021. Anti-CD81 antibodies block vertical transmission of avian leukosis virus subgroup J. Veterinary Microbiology. 264:109293. https://doi.org/10.1016/j.vetmic.2021.109293.

Avian genomics - (Book / Chapter)
Cheng, H.H., Warren, W.C., Zhou, H. 2021. Avian genomics. Book Chapter. In: Scanes, Collin G., Dridi, Sami, editors. Sturkie's Avian Physiology. 7th edition. San Diego, CA: Academic Press. p. 7-16. https://doi.org/10.1016/B978-0-12-819770-7.00047-5.

Viral deubiquitinases and innate antiviral immune response in livestock and poultry - (Peer Reviewed Journal)
Zhou, Z., Xu, J., Li, Z., Lv, Y., Wu, S., Zhang, H., Song, Y., Ai, Y. 2021. Viral deubiquitinases and innate antiviral immune response in livestock and poultry. Journal of Veterinary Medical Science. https://doi.org/10.1292/jvms.21-0199.

Marek’s disease virus telomeric integration profiles of neoplastic host tissues reveal unbiased chromosomal selection and loss of cellular diversity during tumorigenesis - (Peer Reviewed Journal)
Glass, M.C., Smith, J.M., Cheng, H.H., Delany, M.E. 2021. Marek’s disease virus telomeric integration profiles of neoplastic host tissues reveal unbiased chromosomal selection and loss of cellular diversity during tumorigenesis. Genes. 12(10):1630. https://doi.org/10.3390/genes12101630.

Genetic diversity of MHC-BF/BL region in 21 chicken populations - (Peer Reviewed Journal)
Yuan, Y., Zhang, H., Yi, G., You, Z., Zhao, C., Yuan, H., Wang, K., Li, J., Yang, N., Lian, L. 2021. Genetic diversity of MHC-BF/BL region in 21 chicken populations. Frontiers in Genetics. 12:710770. https://doi.org/10.3389/fgene.2021.710770.

3D genomics across the tree of life reveals condensin II as a determinant of architecture type - (Peer Reviewed Journal)
Hoencamp, C., Dudchenko, O., Elbatsh, A.M., Brahmachari, S., Raaijmakers, J.A., Van Schaik, T., Sedeño Cacciatore, A., Contessoto, V., Hildebrandt, E.C., Cheng, H.H., Lieberman Aiden, E., Rowland, B.D. 2021. 3D genomics across the tree of life reveals condensin II as a determinant of architecture type. Science. 372(6545):984-989. https://doi.org/10.1126/science.abe2218.

Tissue resources for the functional annotation of animal genomes - (Peer Reviewed Journal)
Tixier-Boichard, M., Fabre, S., Dhorne-Pollet, S., Goubil, A., Acloque, H., Vincent-Naulleau, S., Ross, P., Wang, Y., Chanthavixay, G., Cheng, H.H., Catherine, E., Leesburg, V.L., Giuffra, E., Zhou, H. 2021. Tissue resources for the functional annotation of animal genomes. Frontiers in Genetics. 12:666265. https://doi.org/10.3389/fgene.2021.666265.

Differential DNA methylation and gene expression between ALV-J-positive and ALV-J-negative chickens - (Peer Reviewed Journal)
Yan, Y., Zhang, H., Gao, S., Zhang, H., Zhang, X., Chen, W., Lin, W., Xie, Q. 2021. Differential DNA methylation and gene expression between ALV-J-positive and ALV-J-negative chickens. Frontiers in Veterinary Science. 8:659840. https://doi.org/10.3389/fvets.2021.659840.

Functional annotations of three domestic animal genomes provide vital resources for comparative and agricultural research - (Peer Reviewed Journal)
Kern, C., Ying, W., Xu, X., Pan, Z., Halstead, M., Chanthavixay, G., Saelao, P., Waters, S., Xiang, R., Chamberlain, A., Korf, I., Delany, M.E., Cheng, H.H., Medrano, J.F., Van Eenennaam, A.L., Tuggle, C.K., Ernst, C., Flicek, P., Quon, G., Ross, P., Zhou, H. 2021. Functional annotations of three domestic animal genomes provide vital resources for comparative and agricultural research. Nature Communications. 12:1821. https://doi.org/10.1038/s41467-021-22100-8.

ALV-J inhibits autophagy through the GADD45ß/MEKK4/P38MAPK signaling pathway and mediates apoptosis following autophagy - (Peer Reviewed Journal)
Liao, Z., Zhang, X., Song, C., Lin, W., Chen, Y., Xie, Z., Chen, S., Nie, Y., Li, A., Zhang, H., Li, H., Li, H., Xie, Q. 2020. ALV-J inhibits autophagy through the GADD45ß/MEKK4/P38MAPK signaling pathway and mediates apoptosis following autophagy. Cell Death & Disease. 11:684. https://doi.org/10.1038/s41419-020-02841-y.

Genome-wide characterization of copy number variations in the host genome in genetic resistance to Marek's disease using next generation sequencing - (Peer Reviewed Journal)
Bai, H., He, Y., Ding, Y., Chu, Q., Lian, L., Heifetz, E.M., Yang, N., Cheng, H.H., Zhang, H., Chen, J., Song, J. 2020. Genome-wide characterization of copy number variations in the host genome in genetic resistance to Marek's disease using next generation sequencing. BMC Genetics. 21:77. https://doi.org/10.1186/s12863-020-00884-w.

Adiponectin and its receptor genes' expression in response to MDV infection of White Leghorns - (Peer Reviewed Journal)
Bai, Y., Yuan, P., Luo, J., Zhang, H., Ramachandran, R., Miao, H., Yang, N., Song, J. 2020. Adiponectin and its receptor genes' expression in response to MDV infection of White Leghorns. Poultry Science. 99(9):4249-4258. https://doi.org/10.1016/j.psj.2020.06.004.

UL36 encoded by Marek’s Disease Virus exhibits linkage-specific deubiquitinase activity - (Peer Reviewed Journal)
Lin, J., Ai, Y., Zhou, H., Lv, Y., Wang, M., Xu, J., Yu, C., Zhang, H., Wang, M. 2020. UL36 encoded by Marek’s Disease Virus exhibits linkage-specific deubiquitinase activity. International Journal of Molecular Sciences. 21(5). https://doi.org/10.3390/ijms21051783.

ADPONECTIN AND ITS RECRPTOR GENES EXPRESSION IN RESPONSE TO MDV INFECTION OF WHITE LEGHORNS - (Abstract Only)

MicroRNA profiling in the bursae of MDV-infected resistant and susceptible chicken lines - (Peer Reviewed Journal)
Heidari, M., Zhang, L., Zhang, H. 2020. MicroRNA profiling in the bursae of MDV-infected resistant and susceptible chicken lines. Genomics. 112:2564-2571. https://doi.org/10.1016/j.ygeno.2020.02.009.

Marek’s disease vaccines-induced differential expression of known and novel microRNAs in primary lymphoid organ bursae of White Leghorn - (Peer Reviewed Journal)
Zhang, L., Zhu, C., Heidari, M., Dong, K., Chang, S., Xie, Q., Zhang, H. 2020. Marek’s disease vaccines-induced differential expression of known and novel microRNAs in primary lymphoid organ bursae of White Leghorn. BioMed Central (BMC) Veterinary Research. 51:19. https://doi.org/10.1186/s13567-020-00746-4.

TRANSCRIPTOMIC PROFILES AND DIFFERENTIAL GENE EXPRESSION OF SPLENIC CD4+ T CELLS IN RESPONSE TO VACCINATION AGAINST MAREK’S DISEASE - (Abstract Only)

Role of the Chicken T Cell Receptor-Beta Repertoire in Genetic Resistance to Marek's Disease - (Abstract Only)

Four cysteine residues contribute to homodimerization of chicken interleukin-2 - (Peer Reviewed Journal)
Deng, C., Tan, H., Zhou, H., Wang, M., Lu, Y., Xu, J., Zhang, H., Han, L., Ai, Y. 2019. Four cysteine residues contribute to homodimerization of chicken interleukin-2. International Journal of Molecular Sciences. 20(22):5744. https://www.doi.org/10.3390/ijms20225744.

Linc-GALMD1 regulates viral gene expression in the chicken - (Peer Reviewed Journal)
He, Y., Han, B., Ding, Y., Zhang, H., Chang, S., Zhang, L., Zhao, C., Yang, N., Song, J. 2019. Linc-GALMD1 regulates viral gene expression in the chicken. Frontiers in Genetics. 10:1122. https://doi.org/10.3389/fgene.2019.01122.

RNA Sequencing revealed differentially expressed genes functionally associated with immunity and tumor suppression during latent phase infection of a vv+MDV in chickens - (Peer Reviewed Journal)
Dong, K., Chang, S., Xie, Q., Zhao, P., Zhang, H. 2019. RNA Sequencing revealed differentially expressed genes functionally associated with immunity and tumor suppression during latent phase infection of a vv+MDV in chickens. Scientific Reports. 9:14182. https://doi.org/10.1038/s41598-019-50561-x.

Allele-specific expression of CD4+ T cells in response to Marek’s disease virus infection - (Peer Reviewed Journal)
Bai, H., He, Y., Ding, Y., Carrillo, J.A., Selvaraj, R.K., Zhang, H., Chen, J., Song, J. 2019. Allele-specific expression of CD4+ T cells in response to Marek’s disease virus infection. Genes. 10(9):718. https://doi.org/10.3390/genes10090718.

Endogenous avian leukosis virus in combination with serotype 2 Marek's disease virus significantly boosted the incidence of lymphoid leukosis-like bursal lymphomas in susceptible chickens - (Peer Reviewed Journal)
Mays, J.K., Black-Pyrkosz, A., Mansour, T., Schutte, B.C., Chang, S., Dong, K., Hunt, H.D., Fadly, A.M., Zhang, L., Zhang, H. 2019. Endogenous avian leukosis virus in combination with serotype 2 Marek’s disease virus boosted the incidence of LL-like bursal lymphomas in susceptible chickens. Journal of Virology. 93:e00861-19. https://doi.org/10.1128/JVI.00861-19.

Marek’s disease virus infection induced mitochondria changes in chickens - (Peer Reviewed Journal)
Chu, Q., Ding, Y., Cai, W., Liu, L., Zhang, H., Song, J. 2019. Marek’s disease virus infection induced mitochondria changes in chickens. International Journal of Molecular Sciences. 20(13): 3150. https://doi.org/10.3390/ijms20133150.

RNA-seq analysis of viral gene expression in the skin of Marek’s disease virus infected chickens - (Peer Reviewed Journal)
Sunkara, L., Ahmad, M., Heidari, M. 2019. RNA-seq analysis of viral gene expression in the skin of Marek’s disease virus infected chickens. Veterinary Immunology and Immunopathology. 213:1-9. https://doi.org/10.1016/j.vetimm.2019.109882.

Marek's Disease-vaccines induced differential expression of microRNAs in the primary lymphoid organ of bursa at 26th day post inoculation. - (Abstract Only)
Zhang, H., Zhang, L., Zhu, C., Kunzhe, D., Heidari, M. 2019. Marek's Disease-vaccines induced differential expression of microRNAs in the primary lymphoid organ of bursa at 26th day post inoculation. Poultry Science Association Meeting Abstract. 98(E-Supplement 1):97.

Grandparental lineage in a reciprocal cross showed no detectable effect on survival days of F2 White Leghorns in response to a very virulent plus Marek’s disease virus challenge - (Peer Reviewed Journal)
Bai, H., He, Y., Ding, Y., Chang, S., Zhang, H., Chen, J., Song, J. 2019. Grandparental lineage in a reciprocal cross showed no detectable effect on survival days of F2 White Leghorns in response to a very virulent plus Marek’s disease virus challenge. Poultry Science. 98.10: 4498-4503. https://doi.org/10.3382/ps/pez209.

Knockout of Atg5 inhibits proliferation and promotes apoptosis of DF-1 cells - (Peer Reviewed Journal)
Liao, Z., Dai, Z., Cai, C., Zhang, X., Li, A., Zhang, H., Yan, Y., Lin, W., Wu, Y., Li, H., Li, H., Xie, Q. 2019. Knockout of Atg5 inhibits proliferation and promotes apoptosis of DF-1 cells. In Vitro Cellular and Developmental Biology - Animals. 55(5):341-348. https://doi.org/10.1007/s11626-019-00342-7.

Circular RNA Vav3 sponges gga-miR-375 to promote epithelial-mesenchymal transition - (Peer Reviewed Journal)
Zhang, X., Yan, Y., Lin, W., Li, A., Zhang, H., Lei, X., Dai, Z., Li, X., Li, H., Chen, W., Chen, F., Ma, J., Xie, Q. 2019. Circular RNA Vav3 sponges gga-miR-375 to promote epithelial-mesenchymal transition. RNA Biology. 16(1):118-132. https://doi.org/10.1080/15476286.2018.1564462.

The emergence of the infection of subgroup J avian leukosis virus escalated the tumor incidence in commercial Yellow chickens in Southern China in recent years - (Peer Reviewed Journal)
Li, H., Wang, P., Lin, L., Shi, M., Gu, Z., Huang, T., Mo, M., Wei, T., Zhang, H., Wei, P. 2018. The emergence of the infection of subgroup J avian leukosis virus escalated the tumor incidence in commercial Yellow chickens in Southern China in recent years. Transboundary and Emerging Diseases. 66(1):312-316. https://doi.org/10.1111/tbed.13023.

Genome-wide identification of tissue-specific long non-coding RNA in three farm animal species - (Peer Reviewed Journal)
Kern, C., Wang, Y., Chitwood, J., Korf, I., DeLany, M., Cheng, H.H., Medrano, J.F., Van Eenennaam, A.L., Ernst, C., Ross, P., Zhou, H. 2018. Genome-wide identification of tissue-specific long non-coding RNA in three farm animal species. BMC Genomics. 19:684. https://doi.org/10.1186/s12864-018-5037-7.

Vaccination and host Marek's disease-resistance genotype significantly reduce oncogenic gallid alphaherpesvirus 2 telomere integration in host birds - (Peer Reviewed Journal)
McPherson, M.C., Cheng, H.H., Smith, J.M., Delany, M.E. 2018. Vaccination and host Marek's disease-resistance genotype significantly reduce oncogenic gallid alphaherpesvirus 2 telomere integration in host birds. Cytogenetics and Genome Research. 156(4):204-214. https://doi.org/10.1159/000495174.

Avian leukosis virus subgroup J attenuates type I interferon production through blocking IkB phosphorylation - (Peer Reviewed Journal)
Lin, W., Xu, Z., Yan, Y., Zhang, H., Li, H., Chen, W., Chen, F., Xie, Q. 2018. Avian leukosis virus subgroup J attenuates type I interferon production through blocking IkB phosphorylation. Frontiers in Microbiology. 9(1089):1-13. https://doi.org/10.3389/fmicb.2018.01089.

Narrowing the wingless-2 mutation to a 227 Kb candidate region on chicken chromosome 12 - (Peer Reviewed Journal)
Webb, A.E., Youngworth, I.A., Kaya, M., Gitter, C.L., O’Hare, E.A., May, B.P., Cheng, H.H., Delany, M.E. 2018. Narrowing the wingless-2 mutation to a 227 Kb candidate region on chicken chromosome 12. Poultry Science. 97(6):1872–1880. https://dx.doi.org/10.3382/ps/pey073.

Identification of aberrantly expressed circRNAs in subgroup J avian leucosis virus induced tumor livers by RNA sequencing - (Peer Reviewed Journal)

Naturally occurring frame-shift mutations in the tvb receptor gene are responsible for decreased susceptibility to subgroups B, D, and E - (Peer Reviewed Journal)
Li, X., Chen, W., Zhang, H., Li, A., Shu, D., Li, H., Dai, Z., Yan, Y., Zhang, X., Lin, W., Ma, J., Xie, Q. 2017. Naturally occurring frame-shift mutations in the tvb receptor gene are responsible for decreased susceptibility to subgroups B, D, and E. Journal of Virology. 92(8):e01770-17. https://doi.org/10.1128/JVI.01770-17.

Poultry Allele-Specific Expression (ASE) of CD4+ T Cells in Response to Marek’s Disease Virus Infection - (Abstract Only)
Bai, H., He, Y., Zhang, H., Song, J. 2018. Poultry Allele-Specific Expression (ASE) of CD4+ T Cells in Response to Marek’s Disease Virus Infection. Annual International Plant & Animal Genome Conference. Paper#0521.