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Pandit S, Sapkota S, Adhikari A, Karki P, Yadav D, Shrestha R, Yogal R, Chalise S, Pathak R, Jha AK. Ethno-geographic distribution and histopathological classification of nasopharyngeal carcinoma in a single center in Nepal. PLoS One 2024; 19:e0304371. [PMID: 38820402 PMCID: PMC11142571 DOI: 10.1371/journal.pone.0304371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 05/10/2024] [Indexed: 06/02/2024] Open
Abstract
INTRODUCTION Nasopharyngeal carcinoma (NPC) shows geographic and ethnic variation with specific etiopathogenesis. This study characterized the distribution of NPC patients stratified by ethnicity, geography, and histology in a tertiary-level cancer center in Nepal. METHODS A descriptive retrospective study was designed to analyze NPC cases from different regions among patients visiting the hospital from 2016 to 2021. Demographic and clinical information was obtained from medical records. Ethical approval was granted by the Nepal Health Research Council (NHRC). Data analyses and visualization were carried out with R software. RESULTS During the six-year period, a total of 65 individuals were diagnosed with NPC, comprising 42 males and 23 females. Patient median age was 43 years (range 11-85 years). A bimodal age distribution of cases was observed with peaks in patients aged 30-39 years and 50-59 years. Of the NPC patients studied, 29 were from Koshi Province, with 7 cases from Ilam district and 6 cases from Morang district. There were 18 patients in Bagmati Province, and Kathmandu district had the highest number of cases within this region, with 8 patients. The highest proportion of cases were observed among patients of Janajati ethnicity (60%), including Rai, Limbu, and Sherpa people. Histologically, undifferentiated non-keratinizing NPC was the most commonly observed subtype, accounting for 43.1% of cases, followed by 20% differentiated non-keratinizing NPC and 4.6% keratinizing NPC across the entire sample population. The majority of patients (75.3%) were diagnosed at an advanced stage (stage III or IV) with none diagnosed at stage I. CONCLUSIONS In our study, most cases of NPC occurred in patients from provinces in eastern Nepal (Koshi province), and of the Janajati ethnic community. The most common histological subtype was undifferentiated non-keratinizing carcinoma. Further epidemiological studies could address differences in prevalence and the challenge of late presentation of NPC patients in Nepal.
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Affiliation(s)
- Subhas Pandit
- Department of Clinical Oncology, Kathmandu Cancer Center, Tathali, Bhaktapur, Nepal
| | - Simit Sapkota
- Department of Clinical Oncology, Kathmandu Cancer Center, Tathali, Bhaktapur, Nepal
| | - Abish Adhikari
- Department of Radiation Oncology, Kathmandu Cancer Center, Tathali, Bhaktapur, Nepal
| | - Prakriti Karki
- Department of Research, Kathmandu Cancer Center, Tathali, Bhaktapur, Nepal
| | - Deepak Yadav
- Department of Head and Neck Oncology, Kathmandu Cancer Center, Tathali, Bhaktapur, Nepal
| | - Roshani Shrestha
- Department of Clinical Oncology, Kathmandu Cancer Center, Tathali, Bhaktapur, Nepal
| | - Rijendra Yogal
- Department of Head and Neck Oncology, Kathmandu Cancer Center, Tathali, Bhaktapur, Nepal
| | - Sanat Chalise
- Department of Pathology, Kathmandu Cancer Center, Tathali, Bhaktapur, Nepal
| | - Rakesh Pathak
- Department of Pathology, Kathmandu Cancer Center, Tathali, Bhaktapur, Nepal
| | - Anjani Kumar Jha
- Department of Radiation Oncology, Kathmandu Cancer Center, Tathali, Bhaktapur, Nepal
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2
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Zhang G, Cui C, Wangdue S, Lu H, Chen H, Xi L, He W, Yuan H, Tsring T, Chen Z, Yang F, Tsering T, Li S, Tashi N, Yang T, Tong Y, Wu X, Li L, He Y, Cao P, Dai Q, Liu F, Feng X, Wang T, Yang R, Ping W, Zhang M, Gao X, Liu Y, Wang W, Fu Q. Maternal genetic history of ancient Tibetans over the past 4000 years. J Genet Genomics 2023; 50:765-775. [PMID: 36933795 DOI: 10.1016/j.jgg.2023.03.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 03/14/2023] [Accepted: 03/14/2023] [Indexed: 03/17/2023]
Abstract
The settlement of the Tibetan Plateau epitomizes human adaptation to a high-altitude environment that poses great challenges to human activity. Here, we reconstruct a 4000-year maternal genetic history of Tibetans using 128 ancient mitochondrial genome data from 37 sites in Tibet. The phylogeny of haplotypes M9a1a, M9a1b, D4g2, G2a'c, and D4i show that ancient Tibetans share the most recent common ancestor with ancient Middle and Upper Yellow River populations around the Early and Middle Holocene. In addition, the connections between Tibetans and Northeastern Asians vary over the past 4000 years, with a stronger matrilineal connection between the two during 4000 BP-3000 BP, and a weakened connection after 3000 BP, that are coincident with climate change, followed by a reinforced connection after the Tubo period (1400 BP-1100 BP). Besides, an over 4000-year matrilineal continuity is observed in some of the maternal lineages. We also find the maternal genetic structure of ancient Tibetans is correlated to the geography and interactions between ancient Tibetans and ancient Nepal and Pakistan populations. Overall, the maternal genetic history of Tibetans can be characterized as a long-term matrilineal continuity with frequent internal and external population interactions that are dynamically shaped by geography, climate changes, as well as historical events.
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Affiliation(s)
- Ganyu Zhang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Can Cui
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shargan Wangdue
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa, Tibet 850000, China
| | - Hongliang Lu
- Center for Archaeological Science, School of Archaeology and Museology, Sichuan University, Chengdu, Sichuan 610064, China
| | - Honghai Chen
- School of Cultural Heritage, Northwest University, Xi'an, Shaanxi 710069, China
| | - Lin Xi
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa, Tibet 850000, China
| | - Wei He
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa, Tibet 850000, China
| | - Haibing Yuan
- Center for Archaeological Science, School of Archaeology and Museology, Sichuan University, Chengdu, Sichuan 610064, China
| | - Tinley Tsring
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa, Tibet 850000, China
| | - Zujun Chen
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa, Tibet 850000, China
| | - Feng Yang
- Center for Archaeological Science, School of Archaeology and Museology, Sichuan University, Chengdu, Sichuan 610064, China
| | - Tashi Tsering
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa, Tibet 850000, China
| | - Shuai Li
- Center for Archaeological Science, School of Archaeology and Museology, Sichuan University, Chengdu, Sichuan 610064, China
| | - Norbu Tashi
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa, Tibet 850000, China
| | - Tsho Yang
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa, Tibet 850000, China
| | - Yan Tong
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa, Tibet 850000, China
| | - Xiaohong Wu
- School of Archaeology and Museology, Peking University, Beijing 100871, China
| | - Linhui Li
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa, Tibet 850000, China
| | - Yuanhong He
- Center for Archaeological Science, School of Archaeology and Museology, Sichuan University, Chengdu, Sichuan 610064, China
| | - Peng Cao
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China
| | - Qingyan Dai
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China
| | - Feng Liu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China
| | - Xiaotian Feng
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China
| | - Tianyi Wang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ruowei Yang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China
| | - Wanjing Ping
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China
| | - Ming Zhang
- School of Cultural Heritage, Northwest University, Xi'an, Shaanxi 710069, China
| | - Xing Gao
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China
| | - Yichen Liu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China.
| | - Wenjun Wang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China; Science and Technology Archaeology, National Centre for Archaeology, Beijing 100013, China.
| | - Qiaomei Fu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China; University of Chinese Academy of Sciences, Beijing 100049, China; Shanghai Qi Zhi Institute, Shanghai 200232, China.
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3
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The matrilineal ancestry of Nepali populations. Hum Genet 2023; 142:167-180. [PMID: 36242641 DOI: 10.1007/s00439-022-02488-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 09/17/2022] [Indexed: 11/04/2022]
Abstract
The Tibetan plateau and high mountain ranges of Nepal are one of the challenging geographical regions inhabited by modern humans. While much of the ethnographic and population-based genetic studies were carried out to investigate the Tibetan and Sherpa highlanders, little is known about the demographic processes that enabled the colonization of the hilly areas of Nepal. Thus, the present study aimed to investigate the past demographic events that shaped the extant Nepalese genetic diversity using mitochondrial DNA (mtDNA) variations from ethnic Nepalese groups. We have analyzed mtDNA sequences of 999 Nepalese and compared data with 38,622 published mtDNA sequences from rest of the world. Our analysis revealed that the genomic landscapes of prehistoric Himalayan settlers of Nepal were similar to that of the low-altitude extant Nepalese (LAN), especially Newar and Magar population groups, but differ from contemporary high-altitude Sherpas. LAN might have derived their East Eurasian ancestry mainly from low-altitude Tibeto-Burmans, who likely have migrated from East Asia and assimilated across the Eastern Himalayas extended from the Eastern Nepal to the North-East of India, Bhutan, Tibet and Northern Myanmar. We also identified a clear genetic sub-structure across different ethnic groups of Nepal based on mtDNA haplogroups and ectodysplasin-A receptor (EDAR) gene polymorphism. Our comprehensive high-resolution mtDNA-based genetic study of Tibeto-Burman communities reconstructs the maternal origins of prehistoric Himalayan populations and sheds light on migration events that have brought most of the East Eurasian ancestry to the present-day Nepalese population.
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4
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Bhandari S, Dolma P, Mukerji M, Prasher B, Montgomery H, Kular D, Jain V, Dadhwal V, Williams DJ, Bhattacharyaa A, Gilbert E, Cavalleri GL, Hillman SL. Population history and genome wide association studies of birth weight in a native high altitude Ladakhi population. PLoS One 2022; 17:e0269671. [PMID: 36126061 PMCID: PMC9488766 DOI: 10.1371/journal.pone.0269671] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 08/04/2022] [Indexed: 11/28/2022] Open
Abstract
Pathological low birth weight due to fetal growth restriction (FGR) is an important predictor of adverse obstetric and neonatal outcomes. It is more common amongst native lowlanders when gestating in the hypoxic environment of high altitude, whilst populations who have resided at high altitude for many generations are relatively protected. Genetic study of pregnant populations at high altitude permits exploration of the role of hypoxia in FGR pathogenesis, and perhaps of FGR pathogenesis more broadly. We studied the umbilical cord blood DNA of 316 neonates born to pregnant women managed at the Sonam Norboo Memorial Hospital, Ladakh (altitude 3540m) between February 2017 and January 2019. Principal component, admixture and genome wide association studies (GWAS) were applied to dense single nucleotide polymorphism (SNP) genetic data, to explore ancestry and genetic predictors of low birth weight. Our findings support Tibetan ancestry in the Ladakhi population, with subsequent admixture with neighboring Indo-Aryan populations. Fetal growth protection was evident in Ladakhi neonates. Although no variants achieved genome wide significance, we observed nominal association of seven variants across genes (ZBTB38, ZFP36L2, HMGA2, CDKAL1, PLCG1) previously associated with birthweight.
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Affiliation(s)
| | - Padma Dolma
- Sonam Norboo Memorial Hospital, Leh, Ladakh, India
| | - Mitali Mukerji
- Council Scientific Industrial Research-Institute for Genomics and Integrative Biology, New Delhi, India
| | - Bhavana Prasher
- Council Scientific Industrial Research-Institute for Genomics and Integrative Biology, New Delhi, India
| | - Hugh Montgomery
- Centre for Human Health and Performance, University College London, London, United Kingdom
| | | | - Vandana Jain
- All India Institute for Medical Sciences, New Delhi, India
| | - Vatsla Dadhwal
- All India Institute for Medical Sciences, New Delhi, India
| | - David J. Williams
- University College London Institute for Women’s Health, London, United Kingdom
| | - Aniket Bhattacharyaa
- Council Scientific Industrial Research-Institute for Genomics and Integrative Biology, New Delhi, India
| | | | | | - Sara L. Hillman
- University College London Institute for Women’s Health, London, United Kingdom
- * E-mail:
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5
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Droma Y, Hanaoka M, Kinjo T, Kobayashi N, Yasuo M, Kitaguchi Y, Ota M. The blunted vascular endothelial growth factor-A (VEGF-A) response to high-altitude hypoxia and genetic variants in the promoter region of the VEGFA gene in Sherpa highlanders. PeerJ 2022; 10:e13893. [PMID: 35996666 PMCID: PMC9392454 DOI: 10.7717/peerj.13893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 07/22/2022] [Indexed: 01/19/2023] Open
Abstract
Background Sherpa highlanders demonstrate extraordinary tolerance to hypoxia at high altitudes, which may be achieved by mechanisms promoting microcirculatory blood flow and capillary density at high altitudes for restoring oxygen supply to tissues. Vascular endothelial growth factors (VEGFs) are important signaling proteins involved in vasculogenesis and angiogenesis which are stimulated by hypoxia. We hypothesize that the VEGF-A, the major member of the VEGF family, and the gene encoding VEGF-A (VEGFA) play a part in the adaptation to high-altitude hypoxia in Sherpa highlanders. Methods Fifty-one Sherpa highlanders in Namche Bazaar village at a high altitude of 3,440 meters (m) above sea level and 76 non-Sherpa lowlanders in Kathmandu city at 1,300 m in Nepal were recruited for the study. Venous blood was sampled to obtain plasma and extract DNA from each subject. The plasma VEGF-A concentrations were measured and five single-nucleotide polymorphisms (SNPs, rs699947, rs833061, rs1570360, rs2010963, and rs3025039) in the VEGFA were genotyped. The VEGF-A levels and allelic frequencies of the SNPs were compared between the two populations. Results A significant difference in oxygen saturation (SpO2) was observed between the two ethnic groups locating at different elevations (93.7 ± 0.2% in Sherpas at 3,440 m vs. 96.7 ± 0.2% in non-Sherpas at 1,300 m, P < 0.05). The plasma VEGF-A concentration in the Sherpas at high altitude was on the same level as that in the non-Sherpas at low altitude (262.8 ± 17.9 pg/ml vs. 266.8 ± 21.8 pg/ml, P = 0.88). This result suggested that the plasma VEGF-A concentration in Sherpa highlanders was stable despite a high-altitude hypoxic stimulus and that therefore the Sherpas exhibited a phenotype of blunted response to hypoxic stress. Moreover, the allele frequencies of the SNPs rs699947, rs833061, and rs2010963 in the promoter region of the VEGFA were different between the Sherpa highlanders and non-Sherpa lowlanders (corrected P values = 3.30 ×10-5, 4.95 ×10-4, and 1.19 ×10-7, respectively). Conclusions Sherpa highlanders exhibited a blunted VEGF-A response to hypoxia at high altitudes, which was speculated to be associated with the distinctive genetic variations of the SNPs and haplotype in the promoter region of VEGFA in Sherpa highlanders.
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Affiliation(s)
- Yunden Droma
- The First Department of Medicine, Shinshu University School of Medicine, Matsumoto, Nagano, Japan
| | - Masayuki Hanaoka
- The First Department of Medicine, Shinshu University School of Medicine, Matsumoto, Nagano, Japan
| | - Takumi Kinjo
- The First Department of Medicine, Shinshu University School of Medicine, Matsumoto, Nagano, Japan
| | - Nobumitsu Kobayashi
- The First Department of Medicine, Shinshu University School of Medicine, Matsumoto, Nagano, Japan
| | - Masanori Yasuo
- The First Department of Medicine, Shinshu University School of Medicine, Matsumoto, Nagano, Japan
| | - Yoshiaki Kitaguchi
- The First Department of Medicine, Shinshu University School of Medicine, Matsumoto, Nagano, Japan
| | - Masao Ota
- Department of Medicine, Division of Hepatology and Gastroenterology, Shinshu University School of Medicine, Matsumoto, Nagano, Japan
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6
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Heiniger G, Walbaum S, Sartori C, Lovis A, Sazzini M, Wellman A, Heinzer R. Altitude-Induced Sleep Apnea Is Highly Dependent on Ethnic Background (Sherpa Vs. Tamang). High Alt Med Biol 2022; 23:165-172. [PMID: 35708530 DOI: 10.1089/ham.2022.0012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Heiniger, Grégory, Simon Walbaum, Claudio Sartori, Alban Lovis, Marco Sazzini, Andrew Wellman, and Raphael Heinzer. Altitude-Induced Sleep Apnea Is Highly Dependent on Ethnic Background (Sherpa Vs. Tamang). High Alt Med Biol. 23:165-172, 2022. Rationale: High altitude-induced hypocapnic alkalosis generates central sleep apnea (CSA). In Nepal, two ethnic groups live at medium-to-high altitude: Tamangs originate from low-altitude Tibeto-Burman populations, whereas Sherpas descend from high-altitude Tibetans. Objective: To compare apnea severity at low and high altitude between Sherpas and Tamangs. Methods: Polygraphy recordings, including airflow and oxygen saturation, were performed in Nepal at "low" (2,030 m) and "high" (4,380 m) altitudes. Resting ventilation (V̇E) and mixed-exhaled CO2 (FECO2) were also measured at the same altitudes. Differences in apnea-hypopnea index (AHI), oxygen desaturation index (ODI), and % of nocturnal periodic breathing (NPB) at the two altitudes were compared between ethnicities. Measurements and Main Results: Twenty Sherpas and 20 Tamangs were included (males, median [interquartile range] age: 24.5 [21.5-27.8] years vs. 26.0 [21.5-39.8] years, body mass index: 23.9 [22.1-26.1] kg/m2 vs. 25.21 [20.6-27.6] kg/m2). Compared with Tamangs, Sherpas showed a lower increase in AHI (+7.5 [2.6-17.2]/h vs. +31.5 [18.2-57.3]/h, p < 0.001), ODI (+13.8 [5.5-28.2]/h vs. +42.0 [22.6-77.6]/h, p < 0.001), and NPB proportion (+0.9 [0-3.5]% vs. +12.8 [3.1-27.4]%, p < 0.001) from low to high altitude. Resting V̇E was higher in Sherpas versus Tamangs at both low (8.45 [6.89-10.70] l/min vs. 6.3 [4.9-8.3] l/min, p = 0.005) and high (9.7 [8.5-11] l/min vs. 8.74 [7.39-9.73] l/min, p = 0.020) altitudes, whereas the mean ± standard deviation FECO2 decrease between low and high altitude was greater in Tamangs versus Sherpas (-0.50% ± 0.44% vs. -0.80% ± 0.33%, p < 0.023). Conclusion: Overall, altitude-adapted Sherpas showed a 3.2-times smaller increase in sleep-disordered breathing between low and high altitude compared with Tamangs, and higher ventilation and a smaller drop in FECO2 at high altitude. These data suggest that genetic differences in breathing control can be protective against CSA.
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Affiliation(s)
- Grégory Heiniger
- Center for Investigation and Research in Sleep, University Hospital of Lausanne, Lausanne, Switzerland
| | - Simon Walbaum
- Department of Internal Medicine and University Hospital of Lausanne, Lausanne, Switzerland
| | - Claudio Sartori
- Department of Internal Medicine and University Hospital of Lausanne, Lausanne, Switzerland
| | - Alban Lovis
- Department of Pulmonary, University Hospital of Lausanne, Lausanne, Switzerland
| | - Marco Sazzini
- Interdepartmental Centre Alma Mater Research Institute on Global Challenges and Climate Change, University of Bologna, Bologna, Italy.,Department of Biological, Geological and Environmental Sciences (BiGeA), Laboratory of Molecular Anthropology and Centre for Genome Biology, University of Bologna, Bologna, Italy
| | - Andrew Wellman
- Division of Sleep Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Raphael Heinzer
- Center for Investigation and Research in Sleep, University Hospital of Lausanne, Lausanne, Switzerland
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7
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Liu CC, Witonsky D, Gosling A, Lee JH, Ringbauer H, Hagan R, Patel N, Stahl R, Novembre J, Aldenderfer M, Warinner C, Di Rienzo A, Jeong C. Ancient genomes from the Himalayas illuminate the genetic history of Tibetans and their Tibeto-Burman speaking neighbors. Nat Commun 2022; 13:1203. [PMID: 35260549 PMCID: PMC8904508 DOI: 10.1038/s41467-022-28827-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 02/14/2022] [Indexed: 12/12/2022] Open
Abstract
Present-day Tibetans have adapted both genetically and culturally to the high altitude environment of the Tibetan Plateau, but fundamental questions about their origins remain unanswered. Recent archaeological and genetic research suggests the presence of an early population on the Plateau within the past 40 thousand years, followed by the arrival of subsequent groups within the past 10 thousand years. Here, we obtain new genome-wide data for 33 ancient individuals from high elevation sites on the southern fringe of the Tibetan Plateau in Nepal, who we show are most closely related to present-day Tibetans. They derive most of their ancestry from groups related to Late Neolithic populations at the northeastern edge of the Tibetan Plateau but also harbor a minor genetic component from a distinct and deep Paleolithic Eurasian ancestry. In contrast to their Tibetan neighbors, present-day non-Tibetan Tibeto-Burman speakers living at mid-elevations along the southern and eastern margins of the Plateau form a genetic cline that reflects a distinct genetic history. Finally, a comparison between ancient and present-day highlanders confirms ongoing positive selection of high altitude adaptive alleles.
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Affiliation(s)
- Chi-Chun Liu
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA
| | - David Witonsky
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA
| | - Anna Gosling
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA.,Department of Anatomy, University of Otago, Dunedin, 9054, New Zealand
| | - Ju Hyeon Lee
- School of Biological Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Harald Ringbauer
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA.,Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Richard Hagan
- Department of Anthropology, University of Oklahoma, Norman, OK, 73019, USA.,Department of Archaeology, University of York, York, YO10 5DD, UK
| | - Nisha Patel
- Department of Plant and Microbiology, University of Oklahoma, Norman, OK, 73019, USA.,Kintai Therapeutics, Cambridge, MA, 02139, USA
| | - Raphaela Stahl
- Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany
| | - John Novembre
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA
| | - Mark Aldenderfer
- Department of Anthropology and Heritage Studies, University of California, Merced, CA, 95343, USA.
| | - Christina Warinner
- Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany. .,Department of Anthropology, Harvard University, Cambridge, MA, 02138, USA.
| | - Anna Di Rienzo
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA.
| | - Choongwon Jeong
- School of Biological Sciences, Seoul National University, Seoul, 08826, Republic of Korea.
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8
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Wang M, Du W, Tang R, Liu Y, Zou X, Yuan D, Wang Z, Liu J, Guo J, Yang X, Chen J, Yang M, Zhang X, Wei LH, Yuan H, Yeh HY, Wang CC, Liu C, He G. Genomic history and forensic characteristics of Sherpa highlanders on the Tibetan Plateau inferred from high-resolution InDel panel and genome-wide SNPs. Forensic Sci Int Genet 2021; 56:102633. [PMID: 34826721 DOI: 10.1016/j.fsigen.2021.102633] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 10/13/2021] [Accepted: 11/10/2021] [Indexed: 11/18/2022]
Abstract
Sherpa people, one of the high-altitude hypoxic adaptive populations, mainly reside in Nepal and the southern Tibet Autonomous Region. The genetic origin and detailed evolutionary profiles of Sherpas remain to be further explored and comprehensively characterized. Here we analyzed the newly-generated InDel genotype data from 628 Dingjie Sherpas by merging with 4222 worldwide InDel profiles and collected genome-wide SNP data (approximately 600K SNPs) from 1612 individuals in 191 modern and ancient populations to explore and reconstruct the fine-scale genetic structure of Sherpas and their relationships with nearby modern and ancient East Asians based on the shared alleles and haplotypes. The forensic parameters of 57 autosomal InDels (A-InDels) included in our used new-generation InDel amplification system showed that this focused InDel panel is informative and polymorphic in Dingjie Sherpas, suggesting that it can be used as the supplementary tool for forensic personal identification and parentage testing in Dingjie Sherpas. Descriptive findings from the PCA, ADMIXTURE, and TreeMix-based phylogenies suggested that studied Nepal Sherpas showed excess allele sharing with neighboring Tibeto-Burman Tibetans. Furthermore, patterns of allele sharing in f-statistics demonstrated that Nepal Sherpas had a different evolutionary history compared with their neighbors from Nepal (Newar and Gurung) but showed genetic similarity with 2700-year-old Chokhopani and modern Tibet Tibetans. QpAdm/qpGraph-based admixture sources and models further showed that Sherpas, core Tibetans, and Chokhopani formed one clade, which could be fitted as having the main ancestry from late Neolithic Qijia millet farmers and other deep ancestries from early Asians. Chromosome painting profiles and shared IBD fragments inferred from fineSTRUCTURE and ChromoPainter not only confirmed the abovementioned genomic affinity patterns but also revealed the fine-scale genetic microstructures among Sino-Tibetan speakers. Finally, natural-selection signals revealed via iHS, nSL and iHH12 showed natural selection signatures associated with disease susceptibility in Sherpas. Generally, we provided the comprehensive landscape of admixture and evolutionary history of Sherpa people based on the shared alleles and haplotypes from the InDel-based genotype data and high-density genome-wide SNP data. The more detailed genetic landscape of Sherpa people should be further confirmed and characterized via ancient genomes or single-molecule real-time sequencing technology.
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Affiliation(s)
- Mengge Wang
- Guangzhou Forensic Science Institute, Guangzhou 510030, PR China; Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, No. 74 Zhongshan Road II, Guangzhou 510080, PR China
| | - Weian Du
- AGCU ScienTech Incorporation, Wuxi 214174, PR China; School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China
| | - Renkuan Tang
- Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing 400016, PR China
| | - Yan Liu
- School of Basic Medical Sciences, North Sichuan Medical College, Nanchong, Sichuan 637100, PR China
| | - Xing Zou
- College of Basic Medicine, Chongqing University, Chongqing 400016, PR China; Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu 610000, PR China
| | - Didi Yuan
- Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing 400016, PR China
| | - Zheng Wang
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu 610000, PR China
| | - Jing Liu
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu 610000, PR China
| | - Jianxin Guo
- Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, State Key Laboratory of Marine Environmental Science, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361005, PR China
| | - Xiaomin Yang
- Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, State Key Laboratory of Marine Environmental Science, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361005, PR China
| | - Jing Chen
- Department of Forensic Medicine, Guizhou Medical University, Guiyang 550000, PR China
| | - Meiqing Yang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang 550000, PR China
| | - Xianpeng Zhang
- Institute of Biological Anthropology, Jinzhou Medical University, Jinzhou 121000, PR China
| | - Lan-Hai Wei
- Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, State Key Laboratory of Marine Environmental Science, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361005, PR China
| | - Haibing Yuan
- National Demonstration Center for Experimental Archaeology Education and Department of Archaeology, Sichuan University, Chengdu 610200, PR China; School of Archaeology and Museology & National Demonstration Center for Experimental Archaeology Education, Sichuan University, Chengdu, Sichuan 610064, PR China.
| | - Hui-Yuan Yeh
- School of Humanities, Nanyang Technological University, Nanyang 639798, Singapore.
| | - Chuan-Chao Wang
- Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, State Key Laboratory of Marine Environmental Science, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361005, PR China.
| | - Chao Liu
- Guangzhou Forensic Science Institute, Guangzhou 510030, PR China; Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, No. 74 Zhongshan Road II, Guangzhou 510080, PR China; School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China.
| | - Guanglin He
- Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, State Key Laboratory of Marine Environmental Science, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361005, PR China; School of Humanities, Nanyang Technological University, Nanyang 639798, Singapore.
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9
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Yang XY, Rakha A, Chen W, Hou J, Qi XB, Shen QK, Dai SS, Sulaiman X, Abdulloevich NT, Afanasevna ME, Ibrohimovich KB, Chen X, Yang WK, Adnan A, Zhao RH, Yao YG, Su B, Peng MS, Zhang YP. Tracing the Genetic Legacy of the Tibetan Empire in the Balti. Mol Biol Evol 2021; 38:1529-1536. [PMID: 33283852 PMCID: PMC8042757 DOI: 10.1093/molbev/msaa313] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The rise and expansion of Tibetan Empire in the 7th to 9th centuries AD affected the course of history across East Eurasia, but the genetic impact of Tibetans on surrounding populations remains undefined. We sequenced 60 genomes for four populations from Pakistan and Tajikistan to explore their demographic history. We showed that the genomes of Balti people from Baltistan comprised 22.6–26% Tibetan ancestry. We inferred a single admixture event and dated it to about 39–21 generations ago, a period that postdated the conquest of Baltistan by the ancient Tibetan Empire. The analyses of mitochondrial DNA, Y, and X chromosome data indicated that both ancient Tibetan males and females were involved in the male-biased dispersal. Given the fact that the Balti people adopted Tibetan language and culture in history, our study suggested the impact of Tibetan Empire on Baltistan involved dominant cultural and minor demic diffusion.
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Affiliation(s)
- Xing-Yan Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, China
| | - Allah Rakha
- Department of Forensic Sciences, University of Health Sciences, Lahore, Pakistan.,Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Wei Chen
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, China.,State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
| | - Juzhi Hou
- Key Laboratory of Alpine Ecology (LAE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China
| | - Xue-Bin Qi
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Quan-Kuan Shen
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Shan-Shan Dai
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Xierzhatijiang Sulaiman
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | | | - Manilova Elena Afanasevna
- E.N. Pavlovsky Institute of Zoology and Parasitology, Academy of Sciences of Republic of Tajikistan, Dushanbe, Tajikistan
| | | | - Xi Chen
- Research Center for Ecology and Environment of Central Asia, Chinese Academy of Sciences, Urumqi, China.,Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
| | - Wei-Kang Yang
- Research Center for Ecology and Environment of Central Asia, Chinese Academy of Sciences, Urumqi, China.,Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
| | - Atif Adnan
- Department of Human Anatomy, School of Basic Medicine, China Medical University, Shenyang, China
| | - Ruo-Han Zhao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Yong-Gang Yao
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China.,KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Bing Su
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Min-Sheng Peng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China.,KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China.,KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
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10
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Szymczak RK, Marosz M, Grzywacz T, Sawicka M, Naczyk M. Death Zone Weather Extremes Mountaineers Have Experienced in Successful Ascents. Front Physiol 2021; 12:696335. [PMID: 34290622 PMCID: PMC8287323 DOI: 10.3389/fphys.2021.696335] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 06/08/2021] [Indexed: 01/15/2023] Open
Abstract
Background Few data are available on mountaineers’ survival prospects in extreme weather above 8000 m (the Death Zone). We aimed to assess Death Zone weather extremes experienced in climbing-season ascents of Everest and K2, all winter ascents of 8000 m peaks (8K) in the Himalayas and Karakoram, environmental records of human survival, and weather extremes experienced with and without oxygen support. Materials and Methods We analyzed 528 ascents of 8K peaks: 423 non-winter ascents without supplemental oxygen (Everest–210, K2–213), 76 ascents in winter without oxygen, and 29 in winter with oxygen. We assessed environmental conditions using the ERA5 dataset (1978–2021): barometric pressure (BP), temperature (Temp), wind speed (Wind), wind chill equivalent temperature (WCT), and facial frostbite time (FFT). Results The most extreme conditions that climbers have experienced with and without supplemental oxygen were: BP 320 hPa (winter Everest) vs. 329 hPa (non-winter Everest); Temp –41°C (winter Everest) vs. –45°C (winter Nanga Parbat); Wind 46 m⋅s–1 (winter Everest) vs. 48 m⋅s–1 (winter Kangchenjunga). The most extreme combined conditions of BP ≤ 333 hPa, Temp ≤ −30°C, Wind ≥ 25 m⋅s–1, WCT ≤ −54°C and FFT ≤ 3 min were encountered in 14 ascents of Everest, two without oxygen (late autumn and winter) and 12 oxygen-supported in winter. The average extreme conditions experienced in ascents with and without oxygen were: BP 326 ± 3 hPa (winter Everest) vs. 335 ± 2 hPa (non-winter Everest); Temp −40 ± 0°C (winter K2) vs. −38 ± 5°C (winter low Karakoram 8K peaks); Wind 36 ± 7 m⋅s–1 (winter Everest) vs. 41 ± 9 m⋅s–1 (winter high Himalayan 8K peaks). Conclusions
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Affiliation(s)
- Robert K Szymczak
- Department of Emergency Medicine, Faculty of Health Sciences, Medical University of Gdańsk, Gdańsk, Poland
| | - Michał Marosz
- Institute of Meteorology and Water Management - National Research Institute, Warsaw, Poland
| | - Tomasz Grzywacz
- Institute of Physical Culture, Kazimierz Wielki University in Bydgoszcz, Bydgoszcz, Poland
| | - Magdalena Sawicka
- Department of Neurology, Faculty of Medicine, Medical University of Gdańsk, Gdańsk, Poland
| | - Marta Naczyk
- Department of Nutritional Biochemistry, Faculty of Health Sciences, Medical University of Gdańsk, Gdańsk, Poland
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11
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Pamenter ME, Hall JE, Tanabe Y, Simonson TS. Cross-Species Insights Into Genomic Adaptations to Hypoxia. Front Genet 2020; 11:743. [PMID: 32849780 PMCID: PMC7387696 DOI: 10.3389/fgene.2020.00743] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Accepted: 06/22/2020] [Indexed: 12/13/2022] Open
Abstract
Over millions of years, vertebrate species populated vast environments spanning the globe. Among the most challenging habitats encountered were those with limited availability of oxygen, yet many animal and human populations inhabit and perform life cycle functions and/or daily activities in varying degrees of hypoxia today. Of particular interest are species that inhabit high-altitude niches, which experience chronic hypobaric hypoxia throughout their lives. Physiological and molecular aspects of adaptation to hypoxia have long been the focus of high-altitude populations and, within the past decade, genomic information has become increasingly accessible. These data provide an opportunity to search for common genetic signatures of selection across uniquely informative populations and thereby augment our understanding of the mechanisms underlying adaptations to hypoxia. In this review, we synthesize the available genomic findings across hypoxia-tolerant species to provide a comprehensive view of putatively hypoxia-adaptive genes and pathways. In many cases, adaptive signatures across species converge on the same genetic pathways or on genes themselves [i.e., the hypoxia inducible factor (HIF) pathway). However, specific variants thought to underlie function are distinct between species and populations, and, in most cases, the precise functional role of these genomic differences remains unknown. Efforts to standardize these findings and explore relationships between genotype and phenotype will provide important clues into the evolutionary and mechanistic bases of physiological adaptations to environmental hypoxia.
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Affiliation(s)
- Matthew E. Pamenter
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
- Ottawa Brain and Mind Research Institute, University of Ottawa, Ottawa, ON, Canada
| | - James E. Hall
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, San Diego, CA, United States
| | - Yuuka Tanabe
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, San Diego, CA, United States
| | - Tatum S. Simonson
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, San Diego, CA, United States
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12
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Gajurel R, Gautam DK, Pun CB, Dhakal HP, Petrovski BÉ, Costea DE, Sapkota D. Trends and clinicopathological characteristics of oral squamous cell carcinomas reported at a tertiary cancer hospital in Nepal during 1999 to 2009. Clin Exp Dent Res 2020; 6:356-362. [PMID: 32488959 PMCID: PMC7301398 DOI: 10.1002/cre2.278] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 12/12/2019] [Accepted: 12/13/2019] [Indexed: 01/05/2023] Open
Abstract
OBJECTIVE Reliable data describing the trends and clinicopathological characteristics of oral squamous cell carcinoma (OSCC) in the Nepalese population are very limited. The current study aimed to examine the demographics, trend, and clinicopathological characteristics of OSCC reported to the main referral/tertiary cancer hospital, the B.P. Koirala Memorial Cancer Hospital (BPKMCH) in Nepal for a period of 11 years (1999-2009). MATERIAL AND METHODS This is a cross-sectional study. Data were retrieved retrospectively from hospital register maintained in the Department of Ear, Nose, Throat at BPKMCH, categorized into demographic and clinicopathological variables and SPSS (V25) was used for the analysis. RESULTS In a period of 11 years, 3,452 cases of head and neck cancer were registered at the Department of Ear, Nose, Throat, BPKMCH. Out of 1,111 oral cancer cases, 1,081 (97.3%) were OSCC. A trend for increasing number of OSCCs presenting to BPKMCH was observed during that period. OSCC was found to be more common among males (73.0%), Brahmin/Chhetri ethnic groups (33.0%), in age group of 51-60 years (31.9%), and in Terai region (62.0%). Tongue (42.8%) was the most common site, followed by buccal mucosa (27.2%). Nevertheless, when stratified with respect to the geographical location and ethnicity, buccal mucosa was the most common site for OSCC in Terai region (63.9%, p = .002) and in Madhesi ethnic group (34.2%, p < .001). Majority of OSCC cases were diagnosed at advanced stage (49.7%, Stage IV) and received a combination therapy (42.0%). CONCLUSIONS Hospital-based records can provide valuable information on disease characteristics in countries like Nepal. This study revealed that the clinicopathological characteristics of OSCC in Nepal follow the global trend. Nevertheless, relationship between specific intraoral sites for OSCC with geographic location and ethnic groups is an interesting observation and requires further population-based studies to clarify these findings.
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Affiliation(s)
- Rashmi Gajurel
- Centre for International HealthUniversity of BergenBergenNorway
- Gade Laboratory for Pathology and Center for Cancer Biomarkers CCBio, Department of Clinical MedicineUniversity of BergenBergenNorway
- Department of Oral Biology, Faculty of DentistryUniversity of OsloOsloNorway
| | - Dej Kumar Gautam
- Department of Surgical Oncology, B.P. Koirala Memorial Cancer HospitalBharatpurNepal
| | - Chin Bahadur Pun
- Department of Pathology, B. P. Koirala Memorial Cancer HospitalBharatpurNepal
| | - Hari Prasad Dhakal
- Department of Pathology and Laboratory Medicine, Nepal Cancer Hospital and Research CentreLalitpurNepal
| | - Beáta Éva Petrovski
- Department of Faculty Administration, IT‐section, Faculty of DentistryUniversity of OsloOsloNorway
| | - Daniela Elena Costea
- Gade Laboratory for Pathology and Center for Cancer Biomarkers CCBio, Department of Clinical MedicineUniversity of BergenBergenNorway
- Department of PathologyHaukeland University HospitalBergenNorway
| | - Dipak Sapkota
- Department of Oral Biology, Faculty of DentistryUniversity of OsloOsloNorway
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13
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Bhandari S, Cavalleri GL. Population History and Altitude-Related Adaptation in the Sherpa. Front Physiol 2019; 10:1116. [PMID: 31555147 PMCID: PMC6722185 DOI: 10.3389/fphys.2019.01116] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 08/12/2019] [Indexed: 12/29/2022] Open
Abstract
The first ascent of Mount Everest by Tenzing Norgay and Sir Edmund Hillary in 1953 brought global attention to the Sherpa people and human performance at altitude. The Sherpa inhabit the Khumbu Valley of Nepal, and are descendants of a population that has resided continuously on the Tibetan plateau for the past ∼25,000 to 40,000 years. The long exposure of the Sherpa to an inhospitable environment has driven genetic selection and produced distinct adaptive phenotypes. This review summarizes the population history of the Sherpa and their physiological and genetic adaptation to hypoxia. Genomic studies have identified robust signals of positive selection across EPAS1, EGLN1, and PPARA, that are associated with hemoglobin levels, which likely protect the Sherpa from altitude sickness. However, the biological underpinnings of other adaptive phenotypes such as birth weight and the increased reproductive success of Sherpa women are unknown. Further studies are required to identify additional signatures of selection and refine existing Sherpa-specific adaptive phenotypes to understand how genetic factors have underpinned adaptation in this population. By correlating known and emerging signals of genetic selection with adaptive phenotypes, we can further reveal hypoxia-related biological mechanisms of adaptation. Ultimately this work could provide valuable information regarding treatments of hypoxia-related illnesses including stroke, heart failure, lung disease and cancer.
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Affiliation(s)
- Sushil Bhandari
- Department of Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Gianpiero L Cavalleri
- Department of Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, Dublin, Ireland
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14
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Witt KE, Huerta-Sánchez E. Convergent evolution in human and domesticate adaptation to high-altitude environments. Philos Trans R Soc Lond B Biol Sci 2019; 374:20180235. [PMID: 31154977 PMCID: PMC6560271 DOI: 10.1098/rstb.2018.0235] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Humans and their domestic animals have lived and thrived in high-altitude environments worldwide for thousands of years. These populations have developed a number of adaptations to survive in a hypoxic environment, and several genomic studies have been conducted to identify the genes that drive these adaptations. Here, we discuss the various adaptations and genetic variants that have been identified as adaptive in human and domestic animal populations and the ways in which convergent evolution has occurred as these populations have adapted to high-altitude environments. We found that human and domesticate populations have adapted to hypoxic environments in similar ways. Specific genes and biological pathways have been involved in high-altitude adaptation for multiple populations, although the specific variants differ between populations. Additionally, we found that the gene EPAS1 is often a target of selection in hypoxic environments and has been involved in multiple adaptive introgression events. High-altitude environments exert strong selective pressures, and human and animal populations have evolved in convergent ways to cope with a chronic lack of oxygen. This article is part of the theme issue ‘Convergent evolution in the genomics era: new insights and directions'.
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Affiliation(s)
- Kelsey E Witt
- 1 Cell and Molecular Biology, University of California-Merced , 5200 Lake Road., Merced, CA 95340 , USA
| | - Emilia Huerta-Sánchez
- 1 Cell and Molecular Biology, University of California-Merced , 5200 Lake Road., Merced, CA 95340 , USA.,2 Ecology and Evolutionary Biology, Brown University , Box G-W, 80 Waterman Street, Providence, RI 02912 , USA.,3 Center for Computational Biology, Brown University , Box G-W, 115 Waterman Street., Providence, RI 02912 , USA
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15
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Heinrich EC, Wu L, Lawrence ES, Cole AM, Anza-Ramirez C, Villafuerte FC, Simonson TS. Genetic variants at the EGLN1 locus associated with high-altitude adaptation in Tibetans are absent or found at low frequency in highland Andeans. Ann Hum Genet 2019; 83:171-176. [PMID: 30719713 DOI: 10.1111/ahg.12299] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 12/03/2018] [Accepted: 12/20/2018] [Indexed: 12/19/2022]
Abstract
EGLN1 encodes the hypoxia-inducible factor (HIF) pathway prolyl hydroxylase 2 (PHD2) that serves as an oxygen-sensitive regulator of HIF activity. The EGLN1 locus exhibits a signature of positive selection in Tibetan and Andean populations and is associated with hemoglobin concentration in Tibetans. Recent reports provide evidence for functional roles of protein-coding variants within the first exon of EGLN1 (rs186996510, rs12097901) that are linked to an adaptive signal in Tibetans, yet whether these same variants are present and contribute to adaptation in Andean highlanders is unknown. We determined the frequencies of these adaptive Tibetan alleles in Quechua Andeans resident at high altitude (4,350 m) in addition to individuals of Nepali ancestry resident at sea level. The rs186996510 C (minor) allele previously found at high frequency in Tibetans is absent in Andean (G: 100%) and rare among Nepali (C: 11.8%, G: 88.2%) cohorts. The minor G allele of rs12097901 is found at similarly low frequencies in Andeans (G: 12.7%, C: 87.3%) and Nepalis (G: 23.5%, C: 76.5%) compared to Tibetans. These results suggest that adaptation involving EGLN1 in Andeans involves different mechanisms than those described in Tibetans. The precise Andean adaptive variants remain to be determined.
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Affiliation(s)
- Erica C Heinrich
- Division of Physiology, Department of Medicine, University of California, San Diego, La Jolla, California
| | - Lu Wu
- Division of Physiology, Department of Medicine, University of California, San Diego, La Jolla, California
| | - Elijah S Lawrence
- Division of Physiology, Department of Medicine, University of California, San Diego, La Jolla, California
| | - Amy M Cole
- Department of Molecular & Cellular Therapeutics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Cecilia Anza-Ramirez
- Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia (UPCH), Lima, Peru
| | | | - Tatum S Simonson
- Division of Physiology, Department of Medicine, University of California, San Diego, La Jolla, California
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16
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Arciero E, Kraaijenbrink T, Asan, Haber M, Mezzavilla M, Ayub Q, Wang W, Pingcuo Z, Yang H, Wang J, Jobling MA, van Driem G, Xue Y, de Knijff P, Tyler-Smith C. Demographic History and Genetic Adaptation in the Himalayan Region Inferred from Genome-Wide SNP Genotypes of 49 Populations. Mol Biol Evol 2018; 35:1916-1933. [PMID: 29796643 PMCID: PMC6063301 DOI: 10.1093/molbev/msy094] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
We genotyped 738 individuals belonging to 49 populations from Nepal, Bhutan, North India, or Tibet at over 500,000 SNPs, and analyzed the genotypes in the context of available worldwide population data in order to investigate the demographic history of the region and the genetic adaptations to the harsh environment. The Himalayan populations resembled other South and East Asians, but in addition displayed their own specific ancestral component and showed strong population structure and genetic drift. We also found evidence for multiple admixture events involving Himalayan populations and South/East Asians between 200 and 2,000 years ago. In comparisons with available ancient genomes, the Himalayans, like other East and South Asian populations, showed similar genetic affinity to Eurasian hunter-gatherers (a 24,000-year-old Upper Palaeolithic Siberian), and the related Bronze Age Yamnaya. The high-altitude Himalayan populations all shared a specific ancestral component, suggesting that genetic adaptation to life at high altitude originated only once in this region and subsequently spread. Combining four approaches to identifying specific positively selected loci, we confirmed that the strongest signals of high-altitude adaptation were located near the Endothelial PAS domain-containing protein 1 and Egl-9 Family Hypoxia Inducible Factor 1 loci, and discovered eight additional robust signals of high-altitude adaptation, five of which have strong biological functional links to such adaptation. In conclusion, the demographic history of Himalayan populations is complex, with strong local differentiation, reflecting both genetic and cultural factors; these populations also display evidence of multiple genetic adaptations to high-altitude environments.
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Affiliation(s)
- Elena Arciero
- The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Thirsa Kraaijenbrink
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Asan
- BGI-Shenzhen, Shenzhen, China
| | - Marc Haber
- The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Massimo Mezzavilla
- The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- Division of Experimental Genetics, Sidra Medical and Research Center, Doha, Qatar
| | - Qasim Ayub
- The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- Tropical Medicine and Biology Multidisciplinary Platform, Monash University Malaysia Genomics Facility, Selangor Darul Ehsan, Malaysia
- School of Science, Monash University Malaysia, Selangor Darul Ehsan, Malaysia
| | | | - Zhaxi Pingcuo
- The Third People’s Hospital of the Tibet Autonomous Region, Lhasa, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen, China
- James D. Watson Institute of Genome Science, Hangzhou, China
| | - Jian Wang
- BGI-Shenzhen, Shenzhen, China
- James D. Watson Institute of Genome Science, Hangzhou, China
| | - Mark A Jobling
- Department of Genetics & Genome Biology, University of Leicester, Leicester, United Kingdom
| | | | - Yali Xue
- The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Peter de Knijff
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Chris Tyler-Smith
- The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
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17
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Blant A, Kwong M, Szpiech ZA, Pemberton TJ. Weighted likelihood inference of genomic autozygosity patterns in dense genotype data. BMC Genomics 2017; 18:928. [PMID: 29191164 PMCID: PMC5709839 DOI: 10.1186/s12864-017-4312-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 11/16/2017] [Indexed: 12/14/2022] Open
Abstract
Background Genomic regions of autozygosity (ROA) arise when an individual is homozygous for haplotypes inherited identical-by-descent from ancestors shared by both parents. Over the past decade, they have gained importance for understanding evolutionary history and the genetic basis of complex diseases and traits. However, methods to infer ROA in dense genotype data have not evolved in step with advances in genome technology that now enable us to rapidly create large high-resolution genotype datasets, limiting our ability to investigate their constituent ROA patterns. Methods We report a weighted likelihood approach for inferring ROA in dense genotype data that accounts for autocorrelation among genotyped positions and the possibilities of unobserved mutation and recombination events, and variability in the confidence of individual genotype calls in whole genome sequence (WGS) data. Results Forward-time genetic simulations under two demographic scenarios that reflect situations where inbreeding and its effect on fitness are of interest suggest this approach is better powered than existing state-of-the-art methods to infer ROA at marker densities consistent with WGS and popular microarray genotyping platforms used in human and non-human studies. Moreover, we present evidence that suggests this approach is able to distinguish ROA arising via consanguinity from ROA arising via endogamy. Using subsets of The 1000 Genomes Project Phase 3 data we show that, relative to WGS, intermediate and long ROA are captured robustly with popular microarray platforms, while detection of short ROA is more variable and improves with marker density. Worldwide ROA patterns inferred from WGS data are found to accord well with those previously reported on the basis of microarray genotype data. Finally, we highlight the potential of this approach to detect genomic regions enriched for autozygosity signals in one group relative to another based upon comparisons of per-individual autozygosity likelihoods instead of inferred ROA frequencies. Conclusions This weighted likelihood ROA inference approach can assist population- and disease-geneticists working with a wide variety of data types and species to explore ROA patterns and to identify genomic regions with differential ROA signals among groups, thereby advancing our understanding of evolutionary history and the role of recessive variation in phenotypic variation and disease. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-4312-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alexandra Blant
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB, Canada
| | - Michelle Kwong
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB, Canada
| | - Zachary A Szpiech
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA
| | - Trevor J Pemberton
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB, Canada.
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