Genetics of Chronic Mountain Sickness in Andean Highlanders

1. Genetics of Chronic Mountain Sickness in Andean Highlanders Nov. 2, 2013 Roy Ronen University of California, San Diego

2. Salt plains (Salar de Uyuni), Bolivia, 3800m Me, circa 2006 Days Years • Chronic Mountain Sickness • Polycythemia • Palpitations • Tinnitus • >> pulmonary hypertension • >> stroke • >> poor birth outcome • … • Acute Mountain Sickness • headaches • fatigue, weakness • dizziness • insomnia • …

3. Positive Darwinian Selection a ‘recent’ example Himalaya Mountains, Tibet Andean Mountains, Peru 58% sea level O2 56% sea level O2 Bale Mountains, Ethiopia 61% sea level O2 • Scheinfeldt et al. 2012 • Alkorta-Aranburu et al. 2012 • Huerta-Sanchez et al. 2013 • Beall et al. 2010 • Bigham et al. 2010 • Simonson et al. 2010 • Yi et al. 2010

4. High Altitude Adaptation Time Andean Mountains, Peru 58% see level O2 migration to high altitude Now High alt. population

5. High Altitude Adaptation Time MRCA migration to high altitude Out-group population Now Low alt. population High alt. population

6. Setup WGS (~30x) of 10 CMS, 10 non-CMS ADMIXTURE, k=4 Control: 66 MXL (Mexican, LA) 1000G, low pass WGS Outgroup: 67 LWK (Luhya, Kenya) 1000G, low pass WGS

7. Setup Arrays Selection Scan few sites(accurate freq.) WGS • Scheinfeldt et al. 2012 • Alkorta-Aranburu et al. 2012 • Huerta-Sanchez et al. 2013 • Beall et al. 2010 • Bigham et al. 2010 • Simonson et al. 2010 • Yi et al. 2010 ‘all’ sites (approx. freq.)

8. Whole Genome Sequencing Chromosome 19, Sπ SNP Frequency Profile (chr19) Whole Genome Sequencing Chromosome 19, Sπ SNP Frequency Profile (chr19) Genotyping Array (Affy 6.0)

9. Genome Wide Scan for Selection Time MRCA migration to high altitude Sπ , Sf , FST, PBS Sπ , Sf , FST, PBS Out-group population Low alt. population High alt. population

10. Chr12, q13.11

11. Known Functions • SENP1 • Regulates GATA1 and HIF1α (!!!) • Senp-/- mice show erythropoiesis defect • PFKM • pfkm deficient mice show hyper vascularization, muscle hypoxia, and exercise intolerance • ANP32D • Oncogene…

12. Experimental Results (1) Measure Expression Fibroblast cell lines derived from CMS & nonCMS Hypoxia 1.5% O2 Normoxia controls

13. Experimental Results (2) RNAi knock down of Drosophila orthologs SENP1 ortholog ANP32D ortholog Condition Normal (21 % O2) Hypoxia (5 % O2) % Survival

14. Summary • WGS important for identifying signature of selection. • New (experimentally validated!) hypoxia-tolerance genes: • Selection of ANP32D, SENP1 in non-CMS (vs. CMS/MXL). • Transcripts highly expressed in CMS vs. non-CMS. • Knock downs remarkably more tolerant to hypoxia. Whole Genome Sequencing Uncovers the Genetic Basis of Chronic Mountain Sickness in Andean Highlanders American Journal of Human Genetics, Sept. 2013

15. Acknowledgments Universidad Peruana Cayetano Heredia • Francisco Villafuerte • David Callacondo UC San Diego • Vineet Bafna Lab • Nitin Udpa • Gabriel Haddad Lab • Dan Zhou • Tsering Stobdan • Huiwen Zhao BGI • Junbin Liang • Yingrui Li • Yi Yin • Yuanping Du • Lixia Guo • Rui Cao • Yu Wang • Xin Jin • Chen Huang • Wenlong Jia • Dandan Cao • Guangwu Guo • Siqi Liu New Mexico HEMC • Otto Appenzeller Vanderbilt Med. Center • Jorge L. Gamboa