Logo Logo

Alika K. Maunakea, PhD

Alika K. Maunakea, Ph.D.


Alika Profile Image
  • Affiliation:
    Department of Native Hawaiian Health
    John A. Burns School of Medicine
    University of Hawaii
  • Phone: (808) 692-1048
  • Email: amaunake@hawaii.edu

Short Bio

Native Hawaiian born and raised in Waiʻanae, Hawaiʻi, Dr. Maunakea received his B.Sc. degree in Biology at Creighton University (2001) and Ph.D. in Biomedical Sciences at the University of California, San Francisco (2008). He completed Postdoctoral training at the National Institutes of Health (2012) and has since joined the John A. Burns School of Medicine at the University of Hawaiʻi, Mānoa (UHM). In studying epigenetics for over 20 years, Dr. Maunakea has made several important contributions that have helped advance the field. In particular, he has developed and applied novel high-throughput, genome-wide technologies that survey DNA methylation and histone modifications, both central components of epigenetic processes, and has discovered novel roles for DNA methylation in regulating alternative promoter usage and in pre-mRNA splicing with implications in disease development. Having been continously supported with several productive NIH grants throughout his career, Dr. Maunakea is currently a Professor in the Department of Anatomy, Biochemistry, and Physiology, where he applies epigenomic information toward understanding the mechanistic relationships of gene-environment interactions that underlie the development of diseases of health disparities as well as promotes diversity in the research workforce. He leads and collaborates with a cadre of clinical, behavioral, economic, and health disparities researchers on various community-based biomedical research projects while simultaneously mentors underrepresented minority students in multidisciplinary research careers.

In response to the COVID-19 pandemic, Dr. Maunakea led efforts to develop infrastructure for community testing and vaccine education to mitigate the adverse impacts of COVID-19 in underserved Native Hawaiian and Pacific Islander (NHPI) populations in Hawaiʻi as part of the NIH-funded Rapid Acceleration of Diagnostics of Underserved Populations (RADxUP) initiative. Notably, he led the development of the first CLIA-certified molecular diagnostics laboratory at a Federally Qualified Health Center in Hawaiʻi serving the largest population of NHPIs in the state. In addition, he established and oversees the Epigenomics Core Facility of Hawaiʻi, the state’s only next-generation sequencing service that integrates this technology with epigenome-wide data of DNA methylation, chromatin structure, histone modifications, and transcriptomic analyses, and bacteria metagenomics for microbiome research. He also directs the Consortium of Research Advancement Facilities and Training (CRAFT), a NIH COBRE-funded resource in the Integrative Center for Precision Nutrition and Human Health at UHM that includes a suite of multiomics core facilities and bioinformatic resources. By integrating these multiomic approaches, Dr. Maunakea seeks to better understand the socioecological determinants that influence epigenomic and gut microbial pathways that regulate inflammatory states that appear to underlie progression of diabetes, the prevalence of which are disproportionately higher among the NHPI population, to identify novel biomarkers that enable prevention in a recent R01-funded study called the Hawaiʻi Social Epigenomics of Early Diabetes (HI-SEED.org). Finally, Dr. Maunakea initiated and leads the Maui Wildfire Exposure Study (www.mauiwes.info), a longtitudinal cohort to better understand the immediate and long-term health impacts of those recovering from the mental/emotional and physical trauma of the wildfires in Lahaina and Kula in August 2023.

Graduate Faculty

Department of Molecular Biosciences and Bioengineering (MBBE)
Department of Public Health Studies (PHS)
Department of Developmental and Reproductive Biology (DRB)
Department of Cell and Molecular Biology (CMB)
Neuroscience Specialization Program, under CMB
Cancer Biology Program (CBP), University of Hawaii, Cancer Center

Research Interests

Applying epigenomic information toward understanding the mechanistic relationships of gene-environment interactions that underlie the development of diseases of health disparities including cardiometabolic and neurodevelopmental conditions.

Using multi-omic approaches, identify novel biomarkers that appear early in disease progression to enable prevention.

Establishing community-academic partnerships for community-engaged biomedical research.

Initiating and maintaining blended, multidisciplinary community-based research with multi-omic biomedical approaches and health services/education that address health disparities.

Selected Publications

• Maunakea AK, Phankitnirundorn K, Peres R, Dye C, Juarez R, Walsh C, Slavens C, Park SL, Wilkens LR, Le Marchand L. Socioeconomic Status, Lifestyle, and DNA Methylation Age Among Racially and Ethnically Diverse Adults: NIMHD Social Epigenomics Program. JAMA Netw Open. 2024 Jul 1;7(7):e2421889. doi: 10.1001/jamanetworkopen.2024.21889. PMID: 39073814; PMCID: PMC11287425.

• Vargas-Maya NI, Maunakea AK, Ramírez-Montiel FB, Sultana R, Peres R, Cervantes QXM, Nieto ALM, Rangel-Serrano Á, Martínez-Álvarez JA, Páramo-Pérez I, Anaya-Velázquez F, Padilla-Vaca F, Franco B. Avirulent UG10 Entamoeba histolytica mutant derived from HM-1:IMSS strain shows limited genome variability and aberrant 5-methyl cytosine genomic distribution. Mol Biochem Parasitol. 2024 Jul 11:111647. doi: 10.1016/j.molbiopara.2024.111647. Epub ahead of print. PMID: 39002760.

• Umeda L, Torres A, Kunihiro BP, Rubas NC, Wells RK, Phankitnirundorn K, Peres R, Juarez R, Maunakea AK. Immuno-Microbial Signature of Vaccine-Induced Immunity against SARS-CoV-2. Vaccines (Basel). 2024 Jun 7;12(6):637. doi: 10.3390/vaccines12060637. PMID: 38932366; PMCID: PMC11209251.

• Allan NP, Yamamoto BY, Kunihiro BP, Nunokawa CKL, Rubas NC, Wells RK, Umeda L, Phankitnirundorn K, Torres A, Peres R, et al. Ketogenic Diet Induced Shifts in the Gut Microbiome Associate with Changes to Inflammatory Cytokines and Brain-Related miRNAs in Children with Autism Spectrum Disorder. Nutrients. 2024; 16(10):1401. https://doi.org/10.3390/nu16101401

• Huang BZ, Binder AM, Quon B, Patel YM, Lum-Jones A, Tiirikainen M, Murphy SE, Loo L, Maunakea AK, Haiman CA, Wilkens LR, Koh WP, Cai Q, Aldrich MC, Siegmund KD, Hecht SS, Yuan JM, Blot WJ, Stram DO, Le Marchand L, Park SL. Epigenome-wide association study of total nicotine equivalents in multiethnic current smokers from three prospective cohorts. Am J Hum Genet. 2024 Mar 7;111(3):456-472. doi: 10.1016/j.ajhg.2024.01.012. Epub 2024 Feb 16. PMID: 38367619.

• Rubas NC, Peres R, Kunihiro BP, Allan NP, Phankitnirundorn K, Wells RK, McCraken TA, Lee RH, Umeda L, Conching A, Juarez R, Maunakea AK. HMGB1 mediates microbiome-immune axis dysregulation underlying reduced neutralization capacity in obesity-related post-acute sequelae of SARS-CoV-2. Scientific Rep. 2024 Jan 3;14(1):355. doi: 10.1038/s41598-023-50027-1. PMID: 38172612; PMCID: PMC10764757.

• Jernigan VBB, Demientieff LX, Maunakea AK. Food Sovereignty as a Path to Health Equity for Indigenous Communities: Introduction to the Focus Issue. Health Promot Pract. 2023 Nov;24(6):1066-1069. doi: 10.1177/15248399231190355. PMID: 37877636.

• Maunakea AK, Juarez R, Maunakea-Forth JK. The Mauli Ola Study: A Unique Academic-Community Partnership With MA'O Organic Farms to Understand and Address Health Inequities Among Native Hawaiians and Other Pacific Islanders in Hawai'i. Health Promot Pract. 2023 Nov;24(6):1087-1090. doi: 10.1177/15248399231190356. PMID: 37877635.

• Becerra CY, Wells RK, Kunihiro BP, Lee RH, Umeda L, Allan NP, Rubas NC, McCracken TA, Nunokawa CKL, Lee MH, Pidlaoan FGS, Phankitnirondorn K, Dye CK, Yamamoto BY, Peres R, Juarez R, Maunakea AK. Examining the immunoepigenetic-gut microbiome axis in the context of self-esteem among Native Hawaiians and other Pacific Islanders. Front Genet. 2023 Apr 19;14:1125217. doi: 10.3389/fgene.2023.1125217. PMID: 37152987; PMCID: PMC10154580.

• Panova N, Allan NP, Rubas NC, Lee RH, Kunihiro BP, Umeda L, Peres R, Juarez R, Maunakea AK. Sequencing the SARS-CoV-2 Genome from Stool Samples of Post-acute Cases Implicates a Novel Mutation Associated with Reduced Antibody Neutralization. Eur J Biomed Res. 2023;2(3):17-23. doi: 10.24018/ejbiomed.2023.2.3.66. Epub 2023 Jul 13. PMID: 37525697; PMCID: PMC10389300.

• Takahashi E, Allan N, Peres R, Ortug A, van der Kouwe AJW, Valli B, Ethier E, Levman J, Baumer N, Tsujimura K, Vargas-Maya NI, McCracken TA, Lee R, Maunakea AK. Integration of structural MRI and epigenetic analyses hint at linked cellular defects of the subventricular zone and insular cortex in autism: Findings from a case study. Front Neurosci. 2023 Feb 3;16:1023665. doi: 10.3389/fnins.2022.1023665. PMID: 36817099; PMCID: PMC9935943.

• Wells RK, Kunihiro BP, Phankitnirundorn K, Peres R, McCracken TA, Umeda L, Lee RH, Kim DY, Juarez R, Maunakea AK. Gut microbial indicators of metabolic health underlie age-related differences in obesity and diabetes risk among Native Hawaiians and Pacific Islanders. Front Cell Infect Microbiol. 2022 Dec 21;12:1035641. doi: 10.3389/fcimb.2022.1035641. PMID: 36619744; PMCID: PMC9812644.

• Baumer Y, Farmer N, Maunakea AK, Needham B, Powell-Wiley TM. Editorial: The biological impact of adversity on cardiovascular disease risk and obesity. Frontiers in Cardiovascular Medicine. 2022 9:1022724. doi: 10.3389/fcvm.2022.1022724

• Juarez R, Phankitnirundorn K, Ramirez A, Peres R; Maunakea AK, Okihiro M. Vaccine-Associated Shifts in SARS-CoV-2 Infectivity among the Native Hawaiian and Other Pacific Islander Population in Hawaii. American Journal of Public Health. 2022 Sep 15:e1-e4. doi: 10.2105/AJPH.2022.306973. Online ahead of print.PMID: 36108254

• Juarez R, Kang Z, Okihiro M, Garcia B, Phankitnirundorn K, Maunakea AK. Dynamics of trust and consumption of COVID-19 information implicate a novel mechanism for COVID-19 vaccine and booster uptake. Vaccines. 2022 Aug 31;10(9):1435. doi: 10.3390/vaccines10091435.PMID: 36146513

• Dye CK, Corley MJ, Ing C, Lum-Jones A, Li D, Mau MKLM, Maunakea AK. Shifts in the immunoepigenomic landscape of monocytes in response to a diabetes-specific social support intervention: a pilot study among Native Hawaiian adults with diabetes. Clin Epigenetics. 2022 Jul 18;14(1):91. doi: 10.1186/s13148-022-01307-6. PMID: 35851422; PMCID: PMC9295496.

• Juarez R, Phankitnirundorn K, Okihiro M, Maunakea AK. Opposing Role of Trust as a Modifier of COVID-19 Vaccine Uptake in an Indigenous Population. Vaccines. 2022 Jun 17;10(6):968. doi: 10.3390/vaccines10060968. PMID: 35746577; PMCID: PMC9229995.

• Juarez R, Siegal N, Maunakea AK. The Effects of COVID-19 Vaccine Mandates in Hawaii. Vaccines. 2022 May 13;10(5):773. doi: 10.3390/vaccines10050773. PMID: 35632529; PMCID: PMC9144874.

• Andrasik MP, Maunakea AK, Oseso L, Rodriguez-Diaz CE, Wallace S, Walters K, Yukawa M. Awakening: The Unveiling of Historically Unaddressed Social Inequities During the COVID-19 Pandemic in the United States. Infect Dis Clin North Am. 2022 Jun;36(2):295-308. doi: 10.1016/j.idc.2022.01.009. Epub 2022 Feb 1. PMID: 35636901; PMCID: PMC8806123.

• Miller CB, Benny P, Riel J, Boushey C, Perez R, Khadka V, Qin Y, Maunakea AK, Lee MJ. Adherence to Mediterranean diet impacts gastrointestinal microbial diversity throughout pregnancy. BMC Pregnancy Childbirth. 2021 Aug 16;21(1):558. doi: 10.1186/s12884-021-04033-8. PMID: 34399704; PMCID: PMC8369757.

• Shiohama T, Ortug A, Alatorre Warren JL, Valli B, Levman J, Faja SK, Tsujimura K, Maunakea AK, Takahashi E. Small nucleus accumbens and large cerebral ventricles in infants and toddlers prior to receiving diagnoses of autism spectrum disorder. Cerebral Cortex. Volume 32, Issue 6, 15 March 2022, Pages 1200–1211, https://doi.org/10.1093/cercor/bhab283.

• Watanabe LM, Hashimoto AC, Torres DJ, Alfulaij N, Peres R, Sultana R, Maunakea AK, Berry MJ, Seale LA. Effect of statin treatment in obese selenium-supplemented mice lacking selenocysteine lyase. Mol Cell Endocrinol. (2021) Aug 1;533:111335. doi: 10.1016/j.mce.2021.111335. Epub 2021 May 27. PMID: 34052303; PMCID: PMC8263501.

• Rubas N, and Maunakea A. Immunoepigenetic-Microbiome Axis: Implications for Health Disparities Research in Native Hawaiians and Pacific Islanders. Hawai'i Journal of Health & Social Welfare (2021) Hawaii J Health Soc Welf. (2021) Aug;80(8):195-198. PMID: 34355196.

• Kunihiro B, Wells R, McCracken T, Kim DY, Peres R, Sultana R, Maunakea A, Supporting Native Hawaiian Health With Community‐Based Social and Biomedical Research. The FASEB Journal (2021) 35:S1. https://doi.org/10.1096/fasebj.2021.35.S1.05291

• Go R. Ross G, Corley M, Petrovich H, Masaki K, Maunakea AK, He Q, Tiirikainen M. Genome-wide epigenetic analyses in Japanese immigrant plantation workers with Parkinson’s Disease and exposure to organochlorines reveal glial genes and pathways involved in neurotoxicity. BMC Neuroscience (2020) 21:31. https://doi.org/10.1186/s12868-020-00582-4

• Leite-Ah Yo K, Avilez K, Hemscheidt T, Ko'omoa Lange D, Maunakea AK. E hō mai ka ʻike kūpuna no ke ola: links between traditional Native Hawaiian concepts of health and epigenetics. Hulili. 2020 vol. 11, no. 2.

• Corley MJ, Vargas-Maya N, Pang APS, Lum-Jones A, Li D, Khadka V, Sultana R, Blanchard DC, Maunakea AK. Epigenetic Delay in the Neurodevelopmental Trajectory of DNA Methylation States in Autism Spectrum Disorders. Front Genet. 2019 Oct 1;10:907. doi: 10.3389/fgene.2019.00907. PMID: 31681403

• Dye CK, Corley MJ, Li D, Khadka VS, Mitchell BI, Sultana R, Lum-Jones A, Shikuma CM, Ndhlovu LC, Maunakea AK. Comparative DNA methylomic analyses reveal potential origins of novel epigenetic biomarkers of insulin resistance in monocytes from virally suppressed HIV-infected adults.
Clin Epigenetics. 2019 Jun 28;11(1):95. doi: 10.1186/s13148-019-0694-1. PMID: 31253200

• Balaan C, Corley MJ, Eulalio T, Leite-Ahyo K, Pang APS, Fang R, Khadka VS, Maunakea AK*, Ward MA*. Juvenile Shank3b deficient mice present with behavioral phenotype relevant to autism spectrum disorder. Behav Brain Res. 2019 Jan 1;356:137-147. doi: 10.1016/j.bbr.2018.08.005. Epub 2018 Aug 19. PMID:30134148, *co-senior authors.

• Park SL, Patel YM, Loo LWM, Mullen DJ, Offringa IA, Maunakea A, Stram DO, Siegmund K, Murphy SE, Tiirikainen M, Le Marchand L. Association of internal smoking dose with blood DNA methylation in three racial/ethnic populations. Clin Epigenetics. 2018 Aug 23;10(1):110. doi: 10.1186/s13148-018-0543-7. PMID:30139389

• Lee RWY, Corley MJ, Pang A, Arakaki G, Abbott L, Nishimoto M, Miyamoto R, Lee E, Yamamoto S, Maunakea AK, Lum-Jones A, Wong M. A modified ketogenic gluten-free diet with MCT improves behavior in children with autism spectrum disorder. Physiol Behav. 2018 May 1;188:205-211. doi: 10.1016/j.physbeh.2018.02.006. PMID:29421589

• Koomoa D and Maunakea AK. Linking traditional native Hawaiian concepts of health with epigenetic research: implications toward developing future indigenous health scientists. In: Lee WK, Look, MA, editors. Hoʻi Hou Ka Mauli Ola: Pathways to Native Hawaiian Health. 5. Honolulu: Hawaiʻinuiākea School of Hawaiian Knowledge and University of Hawaiʻi Press; 2017.

• Pang AP, Sugai C, Maunakea AK. High-throughput sequencing offers new insights into 5-hydroxymethylcytosine. Biomol Concepts. 2016;7(3):169-78. doi: 10.1515/bmc-2016-0011. PubMed PMID: 27356236; PubMed Central PMCID: PMCPMC5433849.

• Fong KS, Hufnagel RB, Khadka VS, Corley MJ, Maunakea AK, Fogelgren B, et al. A mutation in the tuft mouse disrupts TET1 activity and alters the expression of genes that are crucial for neural tube closure. Dis Model Mech. 2016;9(5):585-96. doi: 10.1242/dmm.024109. PubMed PMID: 26989192; PubMed Central PMCID: PMCPMC4892663.

• Corley MJ, Dye C, D'Antoni ML, Byron MM, Leite-Ah Yo K, Lum-Jones A, Nakamoto B, Valcour V, Bandar IS, Shikuma CM, Ndhlovu LC, Maunakea AK. Comparative DNA Methylation Profiling Reveals an Immunoepigenetic Signature of HIV-related Cognitive Impairment. Sci Rep. 2016;6:33310. doi: 10.1038/srep33310. PubMed PMID: 27629381; PubMed Central PMCID: PMCPMC5024304.

• Townsend CK, Dillard A, Hosoda KK, Maskarinec GG, Maunakea AK, Yoshimura SR, et al. Community-Based Participatory Research Integrates Behavioral and Biological Research to Achieve Health Equity for Native Hawaiians. Int J Environ Res Public Health. 2015;13(1):ijerph13010004. doi: 10.3390/ijerph13010004. PubMed PMID: 26703660; PubMed Central PMCID: PMCPMC4730395.

• Corley MJ, Zhang W, Zheng X, Lum-Jones A, Maunakea AK. Semiconductor-based sequencing of genome-wide DNA methylation states. Epigenetics. 2015;10(2):153-66. doi: 10.1080/15592294.2014.1003747. PubMed PMID: 25602802; PubMed Central PMCID: PMCPMC4622511.

• Maunakea AK, Chepelev I, Cui K, Zhao K. Intragenic DNA methylation modulates alternative splicing by recruiting MeCP2 to promote exon recognition. Cell Res. 2013;23(11):1256-69. doi: 10.1038/cr.2013.110. PubMed PMID: 23938295; PubMed Central PMCID: PMCPMC3817542.

• Kraushaar DC*, Jin W*, Maunakea A, Abraham B, Ha M, Zhao K. Genome-wide incorporation dynamics reveal distinct categories of turnover for the histone variant H3.3. Genome Biol. 2013;14(10):R121. doi: 10.1186/gb-2013-14-10-r121. PubMed PMID: 24176123; PubMed Central PMCID: PMCPMC3983652.
*co-first authors.

• Fu H, Maunakea AK, Martin MM, Huang L, Zhang Y, Ryan M, et al. Methylation of histone H3 on lysine 79 associates with a group of replication origins and helps limit DNA replication once per cell cycle. PLoS Genet. 2013;9(6):e1003542. doi: 10.1371/journal.pgen.1003542. PubMed PMID: 23754963; PubMed Central PMCID: PMCPMC3674996.

• Tao Y*, Xi S*, Shan J*, Maunakea A, Che A, Briones V, et al. Lsh, chromatin remodeling family member, modulates genome-wide cytosine methylation patterns at nonrepeat sequences. Proc Natl Acad Sci U S A. 2011;108(14):5626-31. doi: 10.1073/pnas.1017000108. PubMed PMID: 21427231; PubMed Central PMCID: PMCPMC3078362. *co-first authors.

• Maunakea AK, Nagarajan RP, Bilenky M, Ballinger TJ, D'Souza C, Fouse SD, et al. Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature. 2010;466(7303):253-7. doi: 10.1038/nature09165. PubMed PMID: 20613842; PubMed Central PMCID: PMCPMC3998662.

• Maunakea AK, Chepelev I, Zhao K. Epigenome mapping in normal and disease States. Circ Res. 2010;107(3):327-39. doi: 10.1161/CIRCRESAHA.110.222463. PubMed PMID: 20689072; PubMed Central PMCID: PMCPMC2917837.

• Silber J, Lim DA, Petritsch C, Persson AI, Maunakea AK, Yu M, et al. miR-124 and miR-137 inhibit proliferation of glioblastoma multiforme cells and induce differentiation of brain tumor stem cells. BMC Med. 2008;6:14. doi: 10.1186/1741-7015-6-14. PubMed PMID: 18577219; PubMed Central PMCID: PMCPMC2443372.

• Reinhold WC, Reimers MA, Maunakea AK, Kim S, Lababidi S, Scherf U, et al. Detailed DNA methylation profiles of the E-cadherin promoter in the NCI-60 cancer cells. Mol Cancer Ther. 2007;6(2):391-403. doi: 10.1158/1535-7163.MCT-06-0609. PubMed PMID: 17272646.

• Hong C, Maunakea A, Jun P, Bollen AW, Hodgson JG, Goldenberg DD, et al. Shared epigenetic mechanisms in human and mouse gliomas inactivate expression of the growth suppressor SLC5A8. Cancer Res. 2005;65(9):3617-23. doi: 10.1158/0008-5472.CAN-05-0048. PubMed PMID: 15867356.

• Ching TT*, Maunakea AK*, Jun P, Hong C, Zardo G, Pinkel D, et al. Epigenome analyses using BAC microarrays identify evolutionary conservation of tissue-specific methylation of SHANK3. Nat Genet. 2005;37(6):645-51. doi: 10.1038/ng1563. PubMed PMID: 15895082. *co-first authors.

• Reinhold WC, Kouros-Mehr H, Kohn KW, Maunakea AK, Lababidi S, Roschke A, et al. Permissive Apoptosis-Resistance (PAR): A Two-step Model for Development of Resistance to Anticancer Drugs. CCR Frontiers in Science. 2003;2(Sept):2-3. (Note: AACR Journal Publication)

• Reinhold WC, Kouros-Mehr H, Kohn KW, Maunakea AK, Lababidi S, Roschke A, et al. Apoptotic susceptibility of cancer cells selected for camptothecin resistance: gene expression profiling, functional analysis, and molecular interaction mapping. Cancer Res. 2003;63(5):1000-11. PubMed PMID: 12615715.

• Weinstein JN, Scherf U, Lee JK, Nishizuka S, Gwadry F, Bussey AK, Kim S, Smith LH, Tanabe L, Richman S, Alexander J, Kouros-Mehr H, Maunakea A, Reinhold WC. The bioinformatics of microarray gene expression profiling. Cytometry. 2002;47(1):46-9. PubMed PMID: 11774349.

• Wang M, Kikuzaki H, Csiszar K, Boyd CD, Maunakea A, Fong SF, et al. Novel trisaccharide fatty acid ester identified from the fruits of Morinda citrifolia (Noni). J Agric Food Chem. 1999;47(12):4880-2. PubMed PMID: 10606546.

• Boyd C, Maunakea A, Mordan L, Csiszar, K. Polynesian ethnobotanicals: a critical role in new drug discovery. Pacific Health Dialog, Journal of Community Health and Clinical Medicine for the Pacific - The Health of Native Hawaiians. 1998;5(2):337-40.