Periodic Reporting for period 1 - Champagne (Characterisation of high altitude metabolic phenotype driven by unique Andean genetics.)
Reporting period: 2020-10-01 to 2022-09-30
The problem/issue being addressed:
Oxygen is essential for human life, enabling generation of energy to power cellular processes. If there is less oxygen in our body (hypoxia), this stresses our cells and may result in cell death. Hypoxic stress occurs in many diseases of the heart, lung and vascular systems. It can also be experienced at high-altitude, where there is less oxygen in the air. Despite the hypoxic stress of living at high-altitude, human populations have adapted to live and reproduce there. Some of the genetic changes linked to that adaptation have been identified. However, we don’t know how subtle changes in genes help the complex biological problem of chronic hypoxia. Of particular interest are the adaptative changes related to oxidative metabolism, whereby oxygen consumption is required for the breakdown of substrates consumed in the diet to release energy.
Why is it important for society:
Together, my work will further our understanding of the molecular mechanisms critical for tolerance and ultimately survival in hypoxia in all contexts. This includes human adaptation to the high-altitude environment where hypobaric hypoxia threatens human survival, but also highly prevalent hypoxia-related pathological conditions and the metabolic aetiology of these. This includes disease states that span all life stages such as those impacting the heart, lung and circulation and reproductive health.
Overall objectives:
My project is concerned with understanding how genetic variants linked to hypoxic adaptation affect whole-body physiology and metabolism within cells.
Oxygen is essential for human life, enabling generation of energy to power cellular processes. If there is less oxygen in our body (hypoxia), this stresses our cells and may result in cell death. Hypoxic stress occurs in many diseases of the heart, lung and vascular systems. It can also be experienced at high-altitude, where there is less oxygen in the air. Despite the hypoxic stress of living at high-altitude, human populations have adapted to live and reproduce there. Some of the genetic changes linked to that adaptation have been identified. However, we don’t know how subtle changes in genes help the complex biological problem of chronic hypoxia. Of particular interest are the adaptative changes related to oxidative metabolism, whereby oxygen consumption is required for the breakdown of substrates consumed in the diet to release energy.
Why is it important for society:
Together, my work will further our understanding of the molecular mechanisms critical for tolerance and ultimately survival in hypoxia in all contexts. This includes human adaptation to the high-altitude environment where hypobaric hypoxia threatens human survival, but also highly prevalent hypoxia-related pathological conditions and the metabolic aetiology of these. This includes disease states that span all life stages such as those impacting the heart, lung and circulation and reproductive health.
Overall objectives:
My project is concerned with understanding how genetic variants linked to hypoxic adaptation affect whole-body physiology and metabolism within cells.
Results 1: Identification of genetic variants related to metabolic function under selection in the Andean highlander genome
I have utilised Andean (Peruvian) subject whole genome sequence data to identify genetic variants under selective pressure residing within genes that are known regulators of metabolic function. This includes missense single nucleotide variants (SNVs) within the hypoxia inducible factor (EPAS1) and Notch (NOTCH1) signaling systems. The hypoxic inducible factor (HIF) signaling system is a known oxygen sensing system crucial to the cellular hypoxic response that is under selection in highland native populations. Far less is known about the role of Notch signaling system in this context, although evidence suggests it has a crucial role in mediating the hypoxia cellular response. I published a review in February 2022 (https://doi.org/10.3390/life12030437) summarising the current literature on Notch signaling and cross-talk in hypoxia and highlighting this pathway as a candidate for high-altitude adaptation to the wider field.
Results 2: Cellular function downstream of the putatively adaptive EPAS1 variant.
Through precision genome editing, performed in collaboration with Dr Alexis Komor at UCSD, we have introduced the putatively adaptive EPAS1 variant into a human kidney cell line. I have designed a protocol to test the function of this cell line in response to hypoxic stress, through 12 and 24hrs of exposure to either normoxia (21% oxygen) or hypoxia (1% oxygen). Cells carrying the putatively adaptive EPAS1 variant demonstrated lower expression of genes controlled by the HIF systems after 24 hours of hypoxia and suppression of metabolic oxygen consumption alongside mitochondrial morphological changes in both normoxia and hypoxia. The gene expression data is included in a paper submitted in September to the journal Nature Genetics. The metabolic data is ongoing and will be combined into a stand-alone paper. I aim to present this work at the International Hypoxia Symposia, 2023.
Results 3: Association of the putatively adaptive variants in the NOTCH1 gene with metabolic phenotype in the Latino population.
I investigated two putatively adaptive variants within the NOTCH1 gene, both of which are present in lowland Latino populations. In collaboration with Dr Rany Salem at UCSD, we have performed targeted population analysis using a Latino population dataset. Through this, we have identified associations between the NOTCH1 variants and glucose homeostasis. I presented these findings as poster at the Notch signaling Gordon Research Seminar, 2023. In preparation for future experiments into the cellular mechanisms, I have incorporated the variant exhibiting the strongest selection signal into a human cell line.
Results 4: Positive selection signals in the maternal genome reveal placental phenotypes that may preserve fetal oxygenation in Andean highlanders
Using samples and data collected by my collaborator Dr Colleen Julian (University of Colorado) prior to the start of the COVID-19 pandemic, I have examined placental adaptation in the Andean (Bolivian) population and have identified novel links between genetic signatures and placental phenotypes that may preserve oxygenation in Andean highlanders, including association between PTPRD and maximal respiratory capacity in the placenta. A manuscript summarising the results of this work is currently being prepared for submission at the journal PNAS and I am due to present these results.
To note, no specific website has been generated for this project, but details are provided on the website of my host laboratory: https://pulmonary.ucsd.edu/research/labs-centers/simonson/people/index.html
I have utilised Andean (Peruvian) subject whole genome sequence data to identify genetic variants under selective pressure residing within genes that are known regulators of metabolic function. This includes missense single nucleotide variants (SNVs) within the hypoxia inducible factor (EPAS1) and Notch (NOTCH1) signaling systems. The hypoxic inducible factor (HIF) signaling system is a known oxygen sensing system crucial to the cellular hypoxic response that is under selection in highland native populations. Far less is known about the role of Notch signaling system in this context, although evidence suggests it has a crucial role in mediating the hypoxia cellular response. I published a review in February 2022 (https://doi.org/10.3390/life12030437) summarising the current literature on Notch signaling and cross-talk in hypoxia and highlighting this pathway as a candidate for high-altitude adaptation to the wider field.
Results 2: Cellular function downstream of the putatively adaptive EPAS1 variant.
Through precision genome editing, performed in collaboration with Dr Alexis Komor at UCSD, we have introduced the putatively adaptive EPAS1 variant into a human kidney cell line. I have designed a protocol to test the function of this cell line in response to hypoxic stress, through 12 and 24hrs of exposure to either normoxia (21% oxygen) or hypoxia (1% oxygen). Cells carrying the putatively adaptive EPAS1 variant demonstrated lower expression of genes controlled by the HIF systems after 24 hours of hypoxia and suppression of metabolic oxygen consumption alongside mitochondrial morphological changes in both normoxia and hypoxia. The gene expression data is included in a paper submitted in September to the journal Nature Genetics. The metabolic data is ongoing and will be combined into a stand-alone paper. I aim to present this work at the International Hypoxia Symposia, 2023.
Results 3: Association of the putatively adaptive variants in the NOTCH1 gene with metabolic phenotype in the Latino population.
I investigated two putatively adaptive variants within the NOTCH1 gene, both of which are present in lowland Latino populations. In collaboration with Dr Rany Salem at UCSD, we have performed targeted population analysis using a Latino population dataset. Through this, we have identified associations between the NOTCH1 variants and glucose homeostasis. I presented these findings as poster at the Notch signaling Gordon Research Seminar, 2023. In preparation for future experiments into the cellular mechanisms, I have incorporated the variant exhibiting the strongest selection signal into a human cell line.
Results 4: Positive selection signals in the maternal genome reveal placental phenotypes that may preserve fetal oxygenation in Andean highlanders
Using samples and data collected by my collaborator Dr Colleen Julian (University of Colorado) prior to the start of the COVID-19 pandemic, I have examined placental adaptation in the Andean (Bolivian) population and have identified novel links between genetic signatures and placental phenotypes that may preserve oxygenation in Andean highlanders, including association between PTPRD and maximal respiratory capacity in the placenta. A manuscript summarising the results of this work is currently being prepared for submission at the journal PNAS and I am due to present these results.
To note, no specific website has been generated for this project, but details are provided on the website of my host laboratory: https://pulmonary.ucsd.edu/research/labs-centers/simonson/people/index.html
So far, my project has provided insights into the cellular mechanisms of human adaptation to the hypoxia of high-altitude, which can be translated to molecular mechanisms critical for tolerance and ultimately survival in hypoxia in all contexts. This includes highly prevalent hypoxia related pathological conditions. My work considers human function across the lifespan by incorporating the period of pregnancy and development. This includes insight into the highly prevalent placental pathology preeclampsia that threaten the health of the mother and baby.
The association of genetic loci to metabolic functional data extends my work beyond human hypoxia biology to the aetiology of metabolic diseases that are prevalent in high-altitude populations such as chronic mountain sickness and preeclampsia, but also in the wider Latino population, such as type 2 diabetes. Data that provides in-depth insight into metabolic function and related cellular mechanisms in these populations is lacking Latino populatios. My work therefore contributes towards filling this knowledge gap.
My initial results have set the foundations for future proposals where I aim to further investigate the mechanisms underlying the genotype- adaptive metabolic phenotype relationship in high-altitude hypoxia. These are part of career development fellowships, which I am currently applying for, to begin when my current Marie Curie Fellowship is completed.
The association of genetic loci to metabolic functional data extends my work beyond human hypoxia biology to the aetiology of metabolic diseases that are prevalent in high-altitude populations such as chronic mountain sickness and preeclampsia, but also in the wider Latino population, such as type 2 diabetes. Data that provides in-depth insight into metabolic function and related cellular mechanisms in these populations is lacking Latino populatios. My work therefore contributes towards filling this knowledge gap.
My initial results have set the foundations for future proposals where I aim to further investigate the mechanisms underlying the genotype- adaptive metabolic phenotype relationship in high-altitude hypoxia. These are part of career development fellowships, which I am currently applying for, to begin when my current Marie Curie Fellowship is completed.