Mapping Molecular Datasets Back to the Brain Regions They are Extracted from: Remembering the Native Countries of Hypothalamic Expatriates and Refugees

  • Arshad M. KhanEmail author
  • Alice H. Grant
  • Anais Martinez
  • Gully A. P. C. Burns
  • Brendan S. Thatcher
  • Vishwanath T. Anekonda
  • Benjamin W. Thompson
  • Zachary S. Roberts
  • Daniel H. Moralejo
  • James E. Blevins
Part of the Advances in Neurobiology book series (NEUROBIOL, volume 21)


This article focuses on approaches to link transcriptomic, proteomic, and peptidomic datasets mined from brain tissue to the original locations within the brain that they are derived from using digital atlas mapping techniques. We use, as an example, the transcriptomic, proteomic and peptidomic analyses conducted in the mammalian hypothalamus. Following a brief historical overview, we highlight studies that have mined biochemical and molecular information from the hypothalamus and then lay out a strategy for how these data can be linked spatially to the mapped locations in a canonical brain atlas where the data come from, thereby allowing researchers to integrate these data with other datasets across multiple scales. A key methodology that enables atlas-based mapping of extracted datasets—laser-capture microdissection—is discussed in detail, with a view of how this technology is a bridge between systems biology and systems neuroscience.


Hypothalamus Brain atlas Laser-capture microdissection Transcriptomics Proteomics Peptidomics Mapping 



nucleus accumbens




anterodorsal preoptic nucleus


Agouti-Related Peptide


anterior hypothalamic nucleus


anterior hypothalamic nucleus, anterior part


anterior hypothalamic nucleus, central part


anterior hypothalamic nucleus, dorsal part


anterior hypothalamic nucleus, posterior part


area postrema


arcuate hypothalamic nucleus


anterior nuclei, dorsal thalamus


anteroventral preoptic nucleus


anteroventral periventricular nucleus hypothalamus


bed nuclei of the stria terminalis


bed nuclei of the stria terminalis, anterior division, anterolateral area


bed nuclei of the stria terminalis, anterior division, anteromedial area


bed nuclei of the stria terminalis, anterior division, dorsomedial nucleus


bed nuclei of the stria terminalis, anterior division, fusiform nucleus


bed nuclei of the stria terminalis, posterior division, interfascicular nucleus


bed nuclei of the stria terminalis, anterior division, juxtacapsular nucleus


bed nuclei of the stria terminalis, anterior division, magnocellular nucleus


bed nuclei of the stria terminalis, anterior division, oval nucleus


bed nuclei of the stria terminalis, posterior division, principal nucleus


bed nuclei of the stria terminalis, anterior division, rhomboid nucleus


bed nuclei of the stria terminalis, posterior division, transverse nucleus


bed nuclei of the stria terminalis, anterior division, ventral nucleus


anterior commissure




cholecystokinin 1 receptor

Ch. Opt.

optic chiasm


corticotropin-releasing hormone


cholera toxin subunit b


dorsomedial hypothalamic nucleus


enhanced green fluorescent protein






freen fluorescent protein


hypothalamo-neurohypophysial system


internuclear area, hypothalamic periventricular region




laser-capture microdissection


lateral hypothalamic area


lateral hypothalamic area, anterior region, intermediate zone


lateral hypothalamic area, anterior region, ventral zone


lateral hypothalamic area


lateral hypothalamic area, juxtadorsomedial region


lateral hypothalamic area, juxtaparaventricular region


lateral hypothalamic area, juxtaventromedial region, dorsal zone


lateral hypothalamic area, juxtaventromedial region, ventral zone


lateral hypothalamic area, parvicellular region


lateral hypothalamic area, subfornical region, anterior zone


lateral preoptic area


lateral septal nucleus [Cajal]


lateral septal nucleus, caudal part, dorsal zone


lateral septal nucleus, caudal part, ventral zone


lateral septal nucleus, rostral part, dorsolateral zone


lateral septal nucleus, caudal part, medial zone


lateral septal nucleus, rostral part, ventrolateral zone


lateral septal nucleus, ventral part [Risold-Swanson]


melanocortin 4 receptor


median eminence


median eminence, external lamina


median eminence, internal lamina


median preoptic nucleus


midline nuclei, dorsal thalamus


medial mammillary nucleus, body


magnocellular neurons


medial preoptic nucleus


medial preoptic nucleus, central part


medial preoptic nucleus, lateral part


medial preoptic nucleus, medial part


medial preoptic area


medial septal nucleus [Cajal]


diagonal band nucleus [Broca]


neuropeptide Y


nucleus of the solitary tract


optic tract




polymerase chain reaction




dorsal premammillary nucleus


ventral premammillary nucleus




perireuniens nucleus


suprachiasmatic preoptic nucleus


paratenial nucleus


paraventricular hypothalamic nucleus


paraventricular hypothalamic nucleus, descending division


paraventricular hypothalamic nucleus, descending division, forniceal part


paraventricular hypothalamic nucleus, magnocellular division


paraventricular hypothalamic nucleus, medial parvicellular part, dorsal zone


paraventricular hypothalamic nucleus, parvicellular division


paraventricular hypothalamic nucleus, periventricular part


periventricular hypothalamic nucleus, intermediate part


periventricular hypothalamic nucleus, posterior part


preoptic periventricular nucleus


hypothalamic periventricular region


paraventricular thalamic nucleus


quantitative polymerase chain reaction


retrochiasmatic area, lateral hypothalamic area


nucleus reuniens [Malone]


nucleus reuniens, caudal division, dorsal part


nucleus reuniens, caudal division, medial part [Gurdjian]


nucleus reuniens, caudal division, posterior part


RNA integrity number


infundibular stalk


subparaventricular zone hypothalamus


suprachiasmatic nucleus [Spiegel-Zwieg]


subfornical organ


submedial nucleus thalamus


supraoptic hypothalamic nucleus


supraoptic nucleus, retrochiasmatic part


supraoptic commissures


tractus Meynert (fasciculus retroflexus)


tyrosine hydroxylase


tuberal nucleus, intermediate part


tuberal nucleus, subventricular part


tract of Vicq D’Azyr (mammillothalamic tract)

V3 h

third ventricle, hypothalamic part


ventrolateral hypothalamic tract


ventromedial hypothalamic nucleus


ventromedial hypothalamic nucleus, anterior part


ventromedial hypothalamic nucleus, central part


ventromedial hypothalamic nucleus, dorsomedial part


ventromedial hypothalamic nucleus, ventrolateral part




ventral posterolateral nucleus thalamus, principal part


ventral posteromedial nucleus thalamus, principal part





We thank Dr. Sabiha Khan (UTEP) for thoughtful discussion on the organization of the manuscript, and Dr. Harold Gainer (National Institute of Neurological Disorders and Stroke) for his timely feedback. We would like to thank the anonymous reviewer who provided critical and constructive feedback on an earlier draft of this manuscript. We also acknowledge our debt to the late Dr. Claude F. Baxter, who served as Emeritus Professor of Psychiatry and Biobehavioral Sciences at the UCLA Brain Research Institute and past historian of the American Society for Neurochemistry, for having generously provided AMK access to his personal library of seminal works in neurochemistry. His kindness and hospitality are treasured memories. We would also like to acknowledge the contributions of Dr. Rebecca Hull and Nishi Gill for the images provided in Fig. 6.2B, C. Finally, we thank Dr. Alexander C. Jackson (University of Connecticut) for providing us with access to unpublished data from his single-cell transcriptomic studies of neuron populations in the mouse lateral hypothalamic area. This chapter is dedicated to the memory of Dr. John H. Ashe (University of California, Riverside), whose instruction and mentorship have deeply informed this narrative.


Work in the UTEP Systems Neuroscience Laboratory is supported by grants awarded to AMK from the National Institutes of Health (NIH; SC3GM109817 and SC1GM127251), the Howard Hughes Medical Institute (UTEP PERSIST Education Grant; PI: S. Aley), and the UTEP Office of Research and Sponsored Projects (Grand Challenges Award). This work is also supported by funds awarded to the Border Biomedical Research Center by the National Institute of Minority Health and Health Disparities of the NIH (5G12MD007592). AHG is supported by the Research Initiative for Scientific Enhancement (RISE) Graduate Fellowship program of the NIH (R25GM069621). AM has been supported by UTEP PERSIST funds and an NSF GK–12 fellowship. Some data in this study were also based upon work supported by the Office of Research and Development, Medical Research Service, Department of Veterans Affairs (VA); specifically, by Merit Review Awards 1l01BX001213-01A1 and BX004102-01 from the United States (U.S.) Department of Veterans Affairs Biomedical Laboratory Research and Development Service to JEB as well as NIH R01DK115976 to JEB. The contents do not represent the views of the U.S. Department of Veterans Affairs or the U.S. Government. This study was also supported by the University of Washington Diabetes Research Center Cellular and Molecular Imaging Core, which is supported by NIH grant P30DK017047. The contribution by GAPCB to this work was funded by the Defense Advanced Research Projects Agency (DARPA) Big Mechanism program under Army Research Office (ARO) contract W911NF-1-0436 and by NIH grant R01LM012592.


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Copyright information

© Springer International Publishing AG, part of Springer Nature 2018

Authors and Affiliations

  • Arshad M. Khan
    • 1
    • 2
    • 3
    Email author
  • Alice H. Grant
    • 1
    • 2
    • 4
  • Anais Martinez
    • 1
    • 2
    • 4
  • Gully A. P. C. Burns
    • 5
  • Brendan S. Thatcher
    • 6
  • Vishwanath T. Anekonda
    • 6
  • Benjamin W. Thompson
    • 6
  • Zachary S. Roberts
    • 6
  • Daniel H. Moralejo
    • 7
  • James E. Blevins
    • 6
    • 8
  1. 1.UTEP Systems Neuroscience LaboratoryUniversity of Texas at El PasoEl PasoUSA
  2. 2.Department of Biological SciencesUniversity of Texas at El PasoEl PasoUSA
  3. 3.Border Biomedical Research CenterUniversity of Texas at El PasoEl PasoUSA
  4. 4.Graduate Program in PathobiologyUniversity of Texas at El PasoEl PasoUSA
  5. 5.Information Sciences Institute, Viterbi School of Engineering, University of Southern CaliforniaMarina del ReyUSA
  6. 6.VA Puget Sound Health Care System, Office of Research and Development Medical Research Service, Department of Veterans Affairs Medical CenterSeattleUSA
  7. 7.Division of Neonatology, Department of PediatricsUniversity of Washington School of MedicineSeattleUSA
  8. 8.Division of Metabolism, Endocrinology, and Nutrition, Department of MedicineUniversity of Washington School of MedicineSeattleUSA

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