Research

My dissertation investigates the complex relationship between insulin/insulin-like signaling (IIS) and sex-specific gene regulation in Drosophila melanogaster. The IIS pathway plays a key role in regulating metabolism and growth, while also contributing to sex-specific differences in gene expression (SDE). Using a combination of RNA-seq transcriptomics, quantitative genetics, and computational genomics, I characterize how the IIS pathway contributes to sex differences in gene expression across genetic backgrounds and environments.

Dissertation: Sex Differences in the Effects of Hormone Signaling & Endocrine Disruptors in Drosophila melanogaster

Supervisor: Dr. Rita M Graze · Auburn University

My dissertation addresses four interconnected questions about insulin signaling and sex-differential gene expression:

  1. Whether the IIS pathway acts as a simple switch regulating sex-specific expression or functions as a quantitative dial that can be tuned differently in each sex
  2. How genetic variation contributes to distinct patterns of regulatory variation in the pathway and in pathway targets between males and females
  3. Whether differences in regulatory variation between sexes are impacted by changes in environment
  4. To what extent isoform-level regulatory mechanisms, particularly alternative splicing, contribute to sex-differential gene expression patterns

Research Projects

Project 1 — Switch and Dial: Mechanism of IIS Regulation of Sex-Differential Gene Expression

Investigating whether insulin signaling regulates sex-differential gene expression through a switch-like (on/off) or dial-like (quantitative/gradual tuning) mechanism in Drosophila melanogaster head tissues. This project uses RNA-seq with DESeq2, likelihood ratio test (LRT) analysis, CMM analysis, WGCNA, and K-means clustering to characterize the regulatory architecture of the IIS pathway in each sex.

Project 2 — Genotype-by-Sex Interactions in IIS Regulatory Response

Investigating how genetic variation modulates sex-specific regulatory response to insulin signaling perturbation across five DSPR-derived genetic backgrounds. Analysis of 301 RNA-seq samples identified:

  • 1,759 genes responding to IIS perturbation
  • 375 genes with sex-differential responses (90% consistent across genotypes — suggesting resolved sexual conflict)
  • 39 genes with genotype-by-sex interactions (candidates for unresolved sexual conflict)

Project 3 — Genotype-by-Environment Effects on IIS Regulatory Response

Investigating whether insulin signaling modulates the regulatory response to temperature stress (25°C vs 28°C) across genetic backgrounds. Key findings:

  • 181 genes where IIS modulates the temperature response
  • 65 genes show genetic variation in this modulation, enriched for DNA replication/repair functions
  • These genes are associated with latitudinal cline adaptation, linking laboratory findings to natural variation

Project 4 — Sex-Specific Isoform Regulation via Alternative Splicing

Investigating whether sex-differential expression patterns are mediated through alternative splicing using rMATS-turbo analysis across 301 samples and five genetic backgrounds. This project characterizes isoform-level regulatory mechanisms that contribute to sexually dimorphic phenotypes beyond simple changes in total transcript abundance.

Methods & Tools

My research relies on a fully reproducible computational framework:

  • RNA-seq analysis: STAR alignment, DESeq2, LRT analysis, CMM analysis
  • Co-expression: WGCNA (Weighted Gene Co-expression Network Analysis)
  • Alternative splicing: rMATS-turbo
  • Statistical genetics: K-means clustering, pathway enrichment analysis
  • Programming: R, Python, Linux/Unix, Git/GitHub

Selected Publications & Presentations

See the Publications page for a full list.

Peer-Reviewed:

  • Huda, N. et al. (2018). Genetic variation of the transcription factor GATA3, not STAT4, is associated with the risk of type 2 diabetes in the Bangladeshi population. PLoS ONE, 13(7), e0198507.
  • Huda, N. et al. (2021). MNS16A VNTR polymorphism of human telomerase gene. Journal of Diabetes and Its Complications, 35(10), 108018.

Poster Presentations:

  • Huda, N., Graze, R.M. (2023). “The role of insulin signaling in sex differences in gene expression.” 64th Annual Drosophila Research Conference.
  • Huda, N., Washburn, R.C., Williams S.L., Graze, R.M. (2021). “Sex differences in the effects of insulin signaling on food consumption in adult Drosophila melanogaster.” 62nd Annual Drosophila Research Conference.
  • Huda, N., Graze, R.M. (2019). “The contribution of ecdysone signaling to sex differential gene expression in adult Drosophila melanogaster.” 45th Annual SEPEEG.