Abstract
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.
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- ACB:
-
nucleus accumbens
- AchE:
-
acetylcholinesterase
- ADP:
-
anterodorsal preoptic nucleus
- AgRP:
-
Agouti-Related Peptide
- AHN:
-
anterior hypothalamic nucleus
- AHNa:
-
anterior hypothalamic nucleus, anterior part
- AHNc:
-
anterior hypothalamic nucleus, central part
- AHNd:
-
anterior hypothalamic nucleus, dorsal part
- AHNp:
-
anterior hypothalamic nucleus, posterior part
- AP:
-
area postrema
- ARH:
-
arcuate hypothalamic nucleus
- ATN:
-
anterior nuclei, dorsal thalamus
- AVP:
-
anteroventral preoptic nucleus
- AVPV:
-
anteroventral periventricular nucleus hypothalamus
- BST:
-
bed nuclei of the stria terminalis
- BSTal:
-
bed nuclei of the stria terminalis, anterior division, anterolateral area
- BSTam:
-
bed nuclei of the stria terminalis, anterior division, anteromedial area
- BSTdm:
-
bed nuclei of the stria terminalis, anterior division, dorsomedial nucleus
- BSTfu:
-
bed nuclei of the stria terminalis, anterior division, fusiform nucleus
- BSTif:
-
bed nuclei of the stria terminalis, posterior division, interfascicular nucleus
- BSTju:
-
bed nuclei of the stria terminalis, anterior division, juxtacapsular nucleus
- BSTmg:
-
bed nuclei of the stria terminalis, anterior division, magnocellular nucleus
- BSTov:
-
bed nuclei of the stria terminalis, anterior division, oval nucleus
- BSTpr:
-
bed nuclei of the stria terminalis, posterior division, principal nucleus
- BSTrh:
-
bed nuclei of the stria terminalis, anterior division, rhomboid nucleus
- BSTtr:
-
bed nuclei of the stria terminalis, posterior division, transverse nucleus
- BSTv:
-
bed nuclei of the stria terminalis, anterior division, ventral nucleus
- C.a.:
-
anterior commissure
- C.f.d.:
-
fornix
- CCK1R:
-
cholecystokinin 1 receptor
- Ch. Opt.:
-
optic chiasm
- CRH:
-
corticotropin-releasing hormone
- CTB:
-
cholera toxin subunit b
- DMH:
-
dorsomedial hypothalamic nucleus
- EGFP:
-
enhanced green fluorescent protein
- FG:
-
fluorogold
- fx:
-
fornix
- GFP:
-
freen fluorescent protein
- HNS:
-
hypothalamo-neurohypophysial system
- I:
-
internuclear area, hypothalamic periventricular region
- KO:
-
knockout
- LCM:
-
laser-capture microdissection
- LHA:
-
lateral hypothalamic area
- LHAai:
-
lateral hypothalamic area, anterior region, intermediate zone
- LHAav:
-
lateral hypothalamic area, anterior region, ventral zone
- LHAd:
-
lateral hypothalamic area
- LHAjd:
-
lateral hypothalamic area, juxtadorsomedial region
- LHAjp:
-
lateral hypothalamic area, juxtaparaventricular region
- LHAjvd:
-
lateral hypothalamic area, juxtaventromedial region, dorsal zone
- LHAjvv:
-
lateral hypothalamic area, juxtaventromedial region, ventral zone
- LHApc:
-
lateral hypothalamic area, parvicellular region
- LHAsfa:
-
lateral hypothalamic area, subfornical region, anterior zone
- LPO:
-
lateral preoptic area
- LS:
-
lateral septal nucleus [Cajal]
- LSc.d:
-
lateral septal nucleus, caudal part, dorsal zone
- LSc.v:
-
lateral septal nucleus, caudal part, ventral zone
- LSr.dl:
-
lateral septal nucleus, rostral part, dorsolateral zone
- LSr.m:
-
lateral septal nucleus, caudal part, medial zone
- LSr.vl:
-
lateral septal nucleus, rostral part, ventrolateral zone
- LSv:
-
lateral septal nucleus, ventral part [Risold-Swanson]
- MC4-R:
-
melanocortin 4 receptor
- ME:
-
median eminence
- MEex:
-
median eminence, external lamina
- MEin:
-
median eminence, internal lamina
- MEPO:
-
median preoptic nucleus
- MID:
-
midline nuclei, dorsal thalamus
- MM:
-
medial mammillary nucleus, body
- MNs:
-
magnocellular neurons
- MPN:
-
medial preoptic nucleus
- MPNc:
-
medial preoptic nucleus, central part
- MPNl:
-
medial preoptic nucleus, lateral part
- MPNm:
-
medial preoptic nucleus, medial part
- MPO:
-
medial preoptic area
- MS:
-
medial septal nucleus [Cajal]
- NDB:
-
diagonal band nucleus [Broca]
- NPY:
-
neuropeptide Y
- NTS:
-
nucleus of the solitary tract
- opt:
-
optic tract
- OT:
-
oxytocin
- PCR:
-
polymerase chain reaction
- PFA:
-
paraformaldehyde
- PMd:
-
dorsal premammillary nucleus
- PMv:
-
ventral premammillary nucleus
- POMC:
-
pro-opiomelanocortin
- PR:
-
perireuniens nucleus
- PSCH:
-
suprachiasmatic preoptic nucleus
- PT:
-
paratenial nucleus
- PVH:
-
paraventricular hypothalamic nucleus
- PVHd:
-
paraventricular hypothalamic nucleus, descending division
- PVHf:
-
paraventricular hypothalamic nucleus, descending division, forniceal part
- PVHm:
-
paraventricular hypothalamic nucleus, magnocellular division
- PVHmpd:
-
paraventricular hypothalamic nucleus, medial parvicellular part, dorsal zone
- PVHp:
-
paraventricular hypothalamic nucleus, parvicellular division
- PVHpv:
-
paraventricular hypothalamic nucleus, periventricular part
- PVi:
-
periventricular hypothalamic nucleus, intermediate part
- PVp:
-
periventricular hypothalamic nucleus, posterior part
- PVpo:
-
preoptic periventricular nucleus
- PVR:
-
hypothalamic periventricular region
- PVT:
-
paraventricular thalamic nucleus
- qPCR:
-
quantitative polymerase chain reaction
- RCH:
-
retrochiasmatic area, lateral hypothalamic area
- RE:
-
nucleus reuniens [Malone]
- REcd:
-
nucleus reuniens, caudal division, dorsal part
- REcm:
-
nucleus reuniens, caudal division, medial part [Gurdjian]
- REcp:
-
nucleus reuniens, caudal division, posterior part
- RIN:
-
RNA integrity number
- S.t.:
-
infundibular stalk
- SBPV:
-
subparaventricular zone hypothalamus
- SCH:
-
suprachiasmatic nucleus [Spiegel-Zwieg]
- SFO:
-
subfornical organ
- SMT:
-
submedial nucleus thalamus
- SO:
-
supraoptic hypothalamic nucleus
- SOr:
-
supraoptic nucleus, retrochiasmatic part
- sup:
-
supraoptic commissures
- T.M.:
-
tractus Meynert (fasciculus retroflexus)
- TH:
-
tyrosine hydroxylase
- TUi:
-
tuberal nucleus, intermediate part
- TUsv:
-
tuberal nucleus, subventricular part
- V.d’A.:
-
tract of Vicq D’Azyr (mammillothalamic tract)
- V3 h:
-
third ventricle, hypothalamic part
- vlt:
-
ventrolateral hypothalamic tract
- VMH:
-
ventromedial hypothalamic nucleus
- VMHa:
-
ventromedial hypothalamic nucleus, anterior part
- VMHc:
-
ventromedial hypothalamic nucleus, central part
- VMHdm:
-
ventromedial hypothalamic nucleus, dorsomedial part
- VMHvl:
-
ventromedial hypothalamic nucleus, ventrolateral part
- VP:
-
vasopressin
- VPL:
-
ventral posterolateral nucleus thalamus, principal part
- VPM:
-
ventral posteromedial nucleus thalamus, principal part
- μ-array:
-
microarray
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Acknowledgments
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.
Funding
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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Khan, A.M. et al. (2018). Mapping Molecular Datasets Back to the Brain Regions They are Extracted from: Remembering the Native Countries of Hypothalamic Expatriates and Refugees. In: Cheung-Hoi Yu, A., Li, L. (eds) Systems Neuroscience. Advances in Neurobiology, vol 21. Springer, Cham. https://doi.org/10.1007/978-3-319-94593-4_6
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