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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
Chapter
Part of the Advances in Neurobiology book series (NEUROBIOL, volume 21)

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.

Keywords

Hypothalamus Brain atlas Laser-capture microdissection Transcriptomics Proteomics Peptidomics Mapping 

Abbreviations

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

Notes

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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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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