Nikhil Milind

All Publications

• eQTLs identify regulatory networks and drivers of variation in the individual response to sepsis. Cell genomics Burnham, K. L., Milind, N., Lee, W., Kwok, A. J., Cano-Gamez, K., Mi, Y., Geoghegan, C. G., Zhang, P., GAinS Investigators, McKechnie, S., Soranzo, N., Hinds, C. J., Knight, J. C., Davenport, E. E., Addison, J., Galley, H., Hall, S., Roughton, S., Taylor, J., Tennant, H., Webster, N., Guleri, A., Waddington, N., Arawwawala, D., Durcan, J., Mitchell-Inwang, C., Short, A., Smolen, S., Swan, K., Williams, S., Errington, E., Gordon, T., Templeton, M., McCauley, M., Venatesh, P., Ward, G., Baudouin, S., Grier, S., Hall, E., Higham, C., Soar, J., Brett, S., Kitson, D., Moreno, J., Mountford, L., Wilson, R., Hall, P., Hewlett, J., McKechnie, S., Faras-Arraya, R., Garrard, C., Hutton, P., Millo, J., Parsons, P., Smiths, A., Young, D., Raymode, P., Soar, J., Andreou, P., Bowrey, S., Hales, D., Kazembe, S., Rich, N., Roberts, E., Thompson, J., Fletcher, S., Glister, G., Rosbergen, M., Cuesta, J. M., Bion, J., Carrera, R., Lees, S., Millar, J., Mitchell, N., Nilson, A., Perry, E. J., Ruel, S., Wilde, J., Willis, H., Atkinson, J., Brown, A., Jacques, N., Kapila, A., Prowse, H., Bland, M., Bullock, L., Harrison, D., Krige, A., Mills, G., Humphreys, J., Armitage, K., Laha, S., Baldwin, J., Walsh, A., Doherty, N., Drage, S., Ortiz-Ruiz de Gordoa, L., Lowes, S., Higham, C., Walsh, H., Calder, V., Swan, C., Payne, H., Higgins, D., Andrews, S., Mappleback, S., Hinds, C., Watson, D., McLees, E., Purdy, A., Stotz, M., Ochelli-Okpue, A., Bonner, S., Whitehead, I., Hugil, K., Goodridge, V., Cawthor, L., Kuper, M., Pahary, S., Bellingan, G., Marshall, R., Montgomery, H., Ryu, J. H., Bercades, G., Boluda, S., Bentley, A., Mccalman, K., Jefferies, F., Allcock, A., Burnham, K., Davenport, E., Geoghegan, C., Knight, J., Maugeri, N., Mi, Y., Radhakrishnan, J. 2024: 100587

  Abstract

  Sepsis is a clinical syndrome of life-threatening organ dysfunction caused by a dysregulated response to infection, for which disease heterogeneity is a major obstacle to developing targeted treatments. We have previously identified gene-expression-based patient subgroups (sepsis response signatures [SRS]) informative for outcome and underlying pathophysiology. Here, we aimed to investigate the role of genetic variation in determining the host transcriptomic response and to delineate regulatory networks underlying SRS. Using genotyping and RNA-sequencing data on 638 adult sepsis patients, we report 16,049 independent expression (eQTLs) and 32 co-expression module (modQTLs) quantitative trait loci in this disease context. We identified significant interactions between SRS and genotype for 1,578 SNP-gene pairs and combined transcription factor (TF) binding site information (SNP2TFBS) and predicted regulon activity (DoRothEA) to identify candidate upstream regulators. Overall, these approaches identified putative mechanistic links between host genetic variation, cell subtypes, and the individual transcriptomic response to infection.

  View details for DOI 10.1016/j.xgen.2024.100587

  View details for PubMedID 38897207

• Independent and Interactive Effects of Genetic Background and Sex on Tissue Metabolomes of Adipose, Skeletal Muscle, and Liver in Mice METABOLITES Wells, A. E., Barrington, W. T., Dearth, S., Milind, N., Carter, G. W., Threadgill, D. W., Campagna, S. R., Voy, B. H. 2022; 12 (4)

  Abstract

  Genetics play an important role in the development of metabolic diseases. However, the relative influence of genetic variation on metabolism is not well defined, particularly in tissues, where metabolic dysfunction that leads to disease occurs. We used inbred strains of laboratory mice to evaluate the impact of genetic variation on the metabolomes of tissues that play central roles in metabolic diseases. We chose a set of four common inbred strains that have different levels of susceptibility to obesity, insulin resistance, and other common metabolic disorders. At the ages used, and under standard husbandry conditions, these lines are not overtly diseased. Using global metabolomics profiling, we evaluated water-soluble metabolites in liver, skeletal muscle, and adipose from A/J, C57BL/6J, FVB/NJ, and NOD/ShiLtJ mice fed a standard mouse chow diet. We included both males and females to assess the relative influence of strain, sex, and strain-by-sex interactions on metabolomes. The mice were also phenotyped for systems level traits related to metabolism and energy expenditure. Strain explained more variation in the metabolite profile than did sex or its interaction with strain across each of the tissues, especially in liver. Purine and pyrimidine metabolism and pathways related to amino acid metabolism were identified as pathways that discriminated strains across all three tissues. Based on the results from ANOVA, sex and sex-by-strain interaction had modest influence on metabolomes relative to strain, suggesting that the tissue metabolome remains largely stable across sexes consuming the same diet. Our data indicate that genetic variation exerts a fundamental influence on tissue metabolism.

  View details for DOI 10.3390/metabo12040337

  View details for Web of Science ID 000785410200001

  View details for PubMedID 35448524

  View details for PubMedCentralID PMC9031494

• Transcriptomic stratification of late-onset Alzheimer's cases reveals novel genetic modifiers of disease pathology PLOS GENETICS Milind, N., Preuss, C., Haber, A., Ananda, G., Mukherjee, S., John, C., Shapley, S., Logsdon, B. A., Crane, P. K., Carter, G. W. 2020; 16 (6): e1008775

  Abstract

  Late-Onset Alzheimer's disease (LOAD) is a common, complex genetic disorder well-known for its heterogeneous pathology. The genetic heterogeneity underlying common, complex diseases poses a major challenge for targeted therapies and the identification of novel disease-associated variants. Case-control approaches are often limited to examining a specific outcome in a group of heterogenous patients with different clinical characteristics. Here, we developed a novel approach to define relevant transcriptomic endophenotypes and stratify decedents based on molecular profiles in three independent human LOAD cohorts. By integrating post-mortem brain gene co-expression data from 2114 human samples with LOAD, we developed a novel quantitative, composite phenotype that can better account for the heterogeneity in genetic architecture underlying the disease. We used iterative weighted gene co-expression network analysis (WGCNA) to reduce data dimensionality and to isolate gene sets that are highly co-expressed within disease subtypes and represent specific molecular pathways. We then performed single variant association testing using whole genome-sequencing data for the novel composite phenotype in order to identify genetic loci that contribute to disease heterogeneity. Distinct LOAD subtypes were identified for all three study cohorts (two in ROSMAP, three in Mayo Clinic, and two in Mount Sinai Brain Bank). Single variant association analysis identified a genome-wide significant variant in TMEM106B (p-value < 5×10-8, rs1990620G) in the ROSMAP cohort that confers protection from the inflammatory LOAD subtype. Taken together, our novel approach can be used to stratify LOAD into distinct molecular subtypes based on affected disease pathways.

  View details for DOI 10.1371/journal.pgen.1008775

  View details for Web of Science ID 000559723400006

  View details for PubMedID 32492070

  View details for PubMedCentralID PMC7295244