Huntington's disease (HD) patients with anterior cingulate cortex atrophy typically exhibit mood symptomatology. However, the midcingulate cortex's (MCC) role in HD is poorly understood. mRNA sequencing was utilized to examine the MCC transcriptome in HD, and differentially expressed transcripts were validated by NanoString analysis. Transcriptomic analysis of 14 HD patients exhibiting mood, motor, or mixed symptoms revealed differential expression of 223 genes, including several homeo-domain, developmental, and noncoding genes in the MCC. Protein-protein interaction, gene ontology, and cell-type enrichment analyses identified dysregulated pathways in the adult MCC involved in processes linked to embryonic development and organogenesis, epigenetic modification, transcription regulation, neuronal differentiation, and motor system development. Key findings include misexpressed genes associated with limb, muscle and motor neuron development in the motor cohort. These alterations suggest that mutant huntingtin may influence developmental processes via aberrant WNT (Wingless), REST (RE1-silencing transcription factor), and transcription factor signaling, potentially affecting MCC motor function circuitry and neuronal maturation. This study indicates a developmentally associated transcriptional signature in the adult HD MCC that may contribute to altered neuronal function.
WankerEEAstASchindlerF, et al.The pathobiology of perturbed mutant huntingtin protein–protein interactions in Huntington’s disease. J Neurochem2019; 151: 507–519. Preprint at10.1111/jnc.14853.
2.
LiSHLiXJ. Huntingtin-protein interactions and the pathogenesis of Huntington’s disease. Trends Genet2004; 20. Preprint at10.1016/j.tig.2004.01.008.
3.
SnehaNPDharshiniSAPTaguchiYH, et al.Investigating neuron degeneration in Huntington’s disease using RNA-Seq based transcriptome study. Genes (Basel)2023; 14: 1801.
4.
WodaJMCalzonettiTHilditch-MaguireP, et al.Inactivation of the Huntington’s disease gene (Hdh) impairs anterior streak formation and early patterning of the mouse embryo. BMC Dev Biol2005; 5: 17.
5.
GodinJDColomboKyMolina-CalavitaM, et al.Huntingtin is required for mitotic spindle orientation and mammalian neurogenesis. Neuron2010; 67: 392–406.
LimRGSalazarLLWiltonDK, et al.Developmental alterations in Huntington’s disease neural cells and pharmacological rescue in cells and mice. Nat Neurosci2017; 20: 648–660.
8.
Smith-GeaterC, et al.Aberrant development corrected in adult-onset huntington’s disease iPSC-derived neuronal cultures via WNT signaling modulation. Stem Cell Rep2010; 14: 406–419.
9.
ConfortiPBesussoDBocchiVD, et al.Faulty neuronal determination and cell polarization are reverted by modulating HD early phenotypes. Proc Natl Acad Sci USA2018; 115(4): E762–E771. doi: https://doi.org/10.1073/pnas.1715865115
10.
MoleroAEGokhanSGonzalezS, et al.Impairment of developmental stem cell-mediated striatal neurogenesis and pluripotency genes in a knock-in model of huntington’s disease. Proc Natl Acad Sci U S A2009; 106: 21900–21905.
11.
HyeonJWKimAHYanoH. Epigenetic regulation in Huntington’s disease. Neurochem Int2021; 148: 105074.
12.
ValorLMGuirettiDLopez-AtalayaJP, et al.Genomic landscape of transcriptional and epigenetic dysregulation in early onset polyglutamine disease. J Neurosci2013; 33: 10471–10482.
13.
ThuDCVOorschotDETippettLJ, et al.Cell loss in the motor and cingulate cortex correlates with symptomatology in Huntington’s disease. Brain2010; 133: 1094–1110.
FanJHofPRGuiseKG, et al.The functional integration of the anterior cingulate cortex during conflict processing. Cereb Cortex2008; 18: 796–805.
16.
BushGLuuPPosnerMI. Cognitive and emotional influences in anterior cingulate cortex. Trends Cogn Sci2000; 4: 215–222.
17.
BartensteinP, et al.Central motor processing in Huntington’s disease. a PET study. Brain1997; 120: 1553–1567.
18.
ThiruvadyDR, et al.Functional connectivity of the prefrontal cortex in Huntington’s disease. J Neurol Neurosurg Psychiatry2006; 78: 127.
19.
LabadorfAHossAGLagomarsinoV, et al.RNA Sequence analysis of human huntington disease brain reveals an extensive increase in inflammatory and developmental gene expression. PLoS One2015; 10: e0143563.
20.
SteffanJSKazantsevASpasic-BoskovicO, et al.The huntington’s disease protein interacts with p53 and CREB-binding protein and represses transcription. Proc Natl Acad Sci U S A2000; 97: 6763–6768.
WigleJEisenstatD. Homeobox genes in vertebrate forebrain development and disease. Clin Genet2008; 73: 212–226.
23.
MoensCBSelleriL. Hox cofactors in vertebrate development. Dev Biol2006; 291: 193–206.
24.
HumbertS. Is Huntington disease a developmental disorder?EMBO Rep2010; 11: 99.
25.
FunaNSSchachterKALerdrupM, et al.β-Catenin regulates primitive streak induction through collaborative interactions with SMAD2/SMAD3 and OCT4. Cell Stem Cell2015; 16: 639–652.
26.
Moran-RivardLKagawaTSaueressigH, et al.Evx1 is a postmitotic determinant of V0 interneuron identity in the spinal cord. Neuron2001; 29: 385–399.
27.
Juárez-MoralesJLSchulteCJPezoaSA, et al.Evx1 and Evx2 specify excitatory neurotransmitter fates and suppress inhibitory fates through a Pax2-independent mechanism. Neural Dev2016; 11: 5.
28.
BellCCAmaralPPKalsbeekA, et al.The Evx1/Evx1as gene locus regulates anterior-posterior patterning during gastrulation. Sci Rep2016; 6: 26657.
29.
BriataPIlengoCCorteG, et al.The Wnt/β-Catenin→Pitx2 pathway controls the turnover of Pitx2 and other unstable mRNAs. Mol Cell2003; 12: 1201–1211.
30.
EngertSBurtscherILiaoWP, et al.Wnt/β-catenin signalling regulates Sox17 expression and is essential for organizer and endoderm formation in the mouse. Development2013; 140: 3128–3138.
31.
DeLaurierASchweitzerRLoganM. Pitx1 determines the morphology of muscle, tendon, and bones of the hindlimb. Dev Biol2006; 299: 22–34.
32.
DubocV, et al.Tbx4 function during hindlimb development reveals a mechanism that explains the origins of proximal limb defects. Development2021; 148(19): dev199580. doi: https://doi.org/10.1242/dev.199580
33.
InfanteCRParkSMihalaAG, et al.Pitx1 broadly associates with limb enhancers and is enriched on hindlimb cis-regulatory elements. Dev Biol2013; 374: 234–244.
34.
KioussiCBriataPBaekSH, et al.Identification of a Wnt/Dvl/β-Catenin → Pitx2 pathway mediating cell-type-specific proliferation during development. Cell2002; 111: 673–685.
35.
PandeySNCabotageJShiR, et al.Conditional over-expression of PITX1 causes skeletal muscle dystrophy in mice. Biol Open2012; 1: 629–639.
36.
ZhaoJXuY. PITX1 Plays essential functions in cancer. Front Oncol2023; 13: 1253238.
37.
BitsiS, et al.Profound hyperglycemia in knockout mutant mice identifies novel function for POU4F2/Brn-3b in regulating metabolic processes. Am J Physiol Endocrinol Metab2015; 310: E303.
38.
FergusonCAFirulliBAZoiaM, et al.Identification and characterization of Hand2 upstream genomic enhancers active in developing stomach and limbs. Dev Dyn2024; 253: 215–232.
39.
ShenLYuYZhouY, et al.SLC38A2 Provides proline to fulfill unique synthetic demands arising during osteoblast differentiation and bone formation. Elife2022; 11: e76963.
40.
JeannotteLGottiFLandry-TruchonK. Hoxa5: a key player in development and disease. J Dev Biol2016; 4: 13.
41.
WahbaGMHostikkaSLCarpenterEM. The paralogous Hox genes Hoxa10 and Hoxd10 interact to pattern the mouse hindlimb peripheral nervous system and skeleton. Dev Biol2001; 231: 87–102.
42.
De La CruzCCDer-AvakianASpyropoulosDD, et al.Targeted disruption of Hoxd9 and Hoxd10 alters locomotor behavior, vertebral identity, and peripheral nervous system development. Dev Biol1999; 216: 595–610.
MüllerTBrohmannHPieraniA, et al.The homeodomain factor Lbx1 distinguishes two Major programs of neuronal differentiation in the dorsal spinal cord. Neuron2002; 34: 551–562.
45.
WuYWangGScottSA, et al.Hoxc10 and Hoxd10 regulate mouse columnar, divisional and motor pool identity of lumbar motoneurons. Development2008; 135: 171–182.
46.
LeeYYeoISKimN, et al.Transcriptional control of motor pool formation and motor circuit connectivity by the LIM-HD protein Isl2. Elife2023; 12: e84596.
47.
ThalerJPKooSJKaniaA, et al.A postmitotic role for Isl-Class LIM homeodomain proteins in the assignment of visceral spinal motor neuron identity. Neuron2004; 41: 337–350.
48.
CatelaCKratsiosP. Transcriptional mechanisms of motor neuron development in vertebrates and invertebrates. Dev Biol2021; 475: 193–204.
49.
RoyAFranciusCRoussoDL, et al.Onecut transcription factors act upstream of isl1 to regulate spinal motoneuron diversification. Development2012; 139: 3109–3119.
50.
ShahVDrillELance-JonesC. Ectopic expression of Hoxd10 in thoracic spinal segments induces motoneurons with a lumbosacral molecular profile and axon projections to the limb. Dev Dyn2004; 231: 43–56.
51.
LinAWCarpenterEM. Hoxa10 and Hoxd10 coordinately regulate lumbar motor neuron patterning. J Neurobiol2003; 56: 328–337. doi:10.1002/neu.10239
52.
DasenJSLiuJPJessellTM. Motor neuron columnar fate imposed by sequential phases of Hox-c activity. Nature2003; 425: 926–933.
53.
BrohmannHJaglaKBirchmeierC. The role of Lbx1 in migration of muscle precursor cells. Development2000; 127: 437–445.
54.
ChengLSamadOAXuY, et al.Lbx1 and Tlx3 are opposing switches in determining GABAergic versus glutamatergic transmitter phenotypes. Nat Neurosci2005; 8: 1510–1515.
55.
ChengLArataAMizuguchiR, et al.Tlx3 and Tlx1 are post-mitotic selector genes determining glutamatergic over GABAergic cell fates. Nat Neurosci2004; 7: 510–517.
56.
BunnerKDRebecGV. Corticostriatal dysfunction in Huntington’s disease: the basics. Front Hum Neurosci2016; 10: 205914.
57.
SegawaHMiyashitaTHirateY, et al.Functional repression of Islet-2 by disruption of complex with Ldb impairs peripheral axonal outgrowth in embryonic zebrafish. Neuron2001; 30: 423–436.
58.
SunM, et al.Homeobox transcription factor MNX1 is crucial for restraining the expression of pan-neuronal genes in motor neurons. bioRxiv 2021.08.07.455331 (2021).
59.
PhilippiA, et al.Association of autism with polymorphisms in the paired-like homeodomain transcription factor 1 (PITX1) on chromosome 5q31: a candidate gene analysis. BMC Med Genet2007; 8: 1–8.
60.
LakhinaVAreyRNKaletskyR, et al.Genome-wide functional analysis of CREB/long-term memory-dependent transcription reveals distinct basal and memory gene expression programs. Neuron2015; 85: 330–345.
61.
PalumboPAntonaVPalumboO, et al.Variable phenotype in 17q12 microdeletions: clinical and molecular characterization of a new case. Gene2014; 538: 373–378.
62.
RedinaOBabenkoVSmaginD, et al.Gene expression changes in the ventral tegmental area of male mice with alternative social behavior experience in chronic agonistic interactions. Int J Mol Sci2010; 21: 6599.
63.
FoxSRDenerisES. Engrailed is required in maturing serotonin neurons to regulate the cytoarchitecture and survival of the dorsal raphe nucleus. J Neurosci2012; 32: 7832–7842.
64.
GenestineMLinLDurensM, et al.Engrailed-2 (En2) deletion produces multiple neurodevelopmental defects in monoamine systems, forebrain structures and neurogenesis and behavior. Hum Mol Genet2015; 24: 5805–5827.
65.
TouroutoglouAAndreanoJDickersonBC, et al.The tenacious brain: how the anterior mid-cingulate contributes to achieving goals. Cortex2019; 123: 12.
66.
RaoCVFarooquiMZhangY, et al.Spontaneous development of Alzheimer’s disease-associated brain pathology in a Shugoshin-1 mouse cohesinopathy model. Aging Cell2018; 17: e12797.
67.
SinghAPosnerJ. Identification of Comprehensive Genetic Factors, Pathways, and Shared Genetic Architecture of Putamen Volume in Adolescent Cohort. medRxiv (2025). 10.1101/2025.09.24.25336566.
68.
BarnatMCapizziMAparicioE, et al.Huntington’s disease alters human neurodevelopment. Science2010; 369: 787–793.
69.
YamadaHYYaoYWangX, et al.Haploinsufficiency of SGO1 results in deregulated centrosome dynamics, enhanced chromosomal instability and colon tumorigenesis. Cell Cycle2012; 11: 479–488.
70.
ShimizuCFudaHYanaiH, et al.Conservation of the hydroxysteroid sulfotransferase SULT2B1 gene structure in the mouse: pre- and postnatal expression, kinetic analysis of isoforms, and comparison with prototypical SULT2A1. Endocrinology2003; 144: 1186–1193.
71.
CarverCMReddyDS. Neurosteroid interactions with synaptic and extrasynaptic GABAa receptors: regulation of subunit plasticity, phasic and tonic inhibition, and neuronal network excitability. Psychopharmacology (Berl)2013; 230: 151–188.
72.
MontenegroYHAde Queiroga NascimentoDde AssisTO, et al.The epigenetics of the hypothalamic-pituitary-adrenal axis in fetal development. Ann Hum Genet2019; 83: 195–213.
73.
KioussiCCarrièreCRosenfeldMG. A model for the development of the hypothalamic–pituitary axis: transcribing the hypophysis. Mech Dev1999; 81: 23–35.
74.
GagePJSuhHCamperSA. Dosage requirement of Pitx2 for development of multiple organs. Development1999; 126: 4643–4651.
75.
ChengJLiuHPLinWY, et al.Identification of contributing genes of Huntington’s disease by machine learning. BMC Med Genomics2010; 13.
76.
SimeoneAD'ApiceMRNigroV, et al.Orthopedia, a novel homeobox-containing gene expressed in the developing CNS of both mouse and Drosophila. Neuron1994; 13: 83–101.
77.
Farooqui-KabirSRDissJKJHendersonD, et al.Cardiac expression of Brn-3a and Brn-3b POU transcription factors and regulation of Hsp27 gene expression. Cell Stress Chaperones2008; 13: 297–312.
78.
HeXTreacyMNSimmonsDM, et al.Expression of a large family of POU-domain regulatory genes in mammalian brain development. Nature1989; 340: 35–42.
79.
Budhram-MahadeoV. The closely related POU family transcription factors Brn-3a and Brn-3b are expressed in distinct cell types in the testis. Int J Biochem Cell Biol2001; 33: 1027–1039.
80.
PanLYangZFengL, et al.Functional equivalence of Brn3 POU-domain transcription factors in mouse retinal neurogenesis. Development2005; 132: 703–712.
81.
Budhram-MahadeoVFujitaRBitsiS, et al.Co-expression of POU4F2/Brn-3b with p53 may be important for controlling expression of pro-apoptotic genes in cardiomyocytes following ischaemic/hypoxic insults. Cell Death Dis2014; 5: e1503–e1503.
82.
TogherKLTogherKLO'KeeffeMM, et al.Epigenetic regulation of the placental HSD11B2 barrier and its role as a critical regulator of fetal development. Epigenetics2014; 9: 816–822.
83.
GuoSZhangYZhouT, et al.GATA4 As a novel regulator involved in the development of the neural crest and craniofacial skeleton via Barx1. Cell Death Differ2018; 25: 1996–2009.
84.
WatersJAUrbanoIRobinsonM, et al.Insulin-like growth factor binding protein 5: diverse roles in cancer. Front Oncol2022; 12: 1052457.
85.
RouillardADGundersenGWFernandezNF, et al.The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins. Database2016; 2016: baw100.
86.
JinLLiuYWuY, et al.REST Is not resting: REST/NRSF in health and disease. Biomolecules2023; 13: 1477.
87.
BallasNGrunseichCLuDD, et al.REST And its corepressors mediate plasticity of neuronal gene chromatin throughout neurogenesis. Cell2005; 121: 645–657.
88.
ChenZFPaquetteAJAndersonDJ. NRSF/REST is required in vivo for repression of multiple neuronal target genes during embryogenesis. Nat Genet1998; 20: 136–142.
89.
DattaMBhattacharyyaNP. Regulation of RE1 protein silencing transcription factor (REST) expression by HIP1 protein interactor (HIPPI). J Biol Chem2011; 286: 33759–33769.
90.
VaughanOR, et al.Placenta-specific Slc38a2/SNAT2 knockdown causes fetal growth restriction in mice. Clin Sci (Lond)2021; 135: 2046–2066.
91.
KerschbamerEBiagioliM. Huntington’s disease as neurodevelopmental disorder: altered chromatin regulation, coding, and non-coding RNA transcription. Front Neurosci2016; 9: 509.
92.
SinhaMMukhopadhyaySBhattacharyyaNP. Mechanism(s) of alteration of micro rna expressions in huntington’s disease and their possible contributions to the observed cellular and molecular dysfunctions in the disease. Neuromolecular Med2012; 14: 221–243.
93.
SalemiMSchillaciFASalluzzoMG, et al.Dysregulation of miRNAs in sicilian patients with huntington’s disease. Diagnostics2025; 15: 2454.
94.
BaeB.IlXuHIgarashiS, et al. P53 mediates cellular dysfunction and behavioral abnormalities in Huntington’s disease. Neuron2005; 47: 29–41.
95.
RajkumarAPQvistPLazarusR, et al.Experimental validation of methods for differential gene expression analysis and sample pooling in RNA-Seq. BMC Genomics2015; 16: 548. doi: https://doi.org/10.1186/s12864-015-1767-y
96.
TereshchenkoA, et al.Developmental trajectory of height, weight, and BMI in children and adolescents at risk for huntington’s disease: effect of mHTT on growth. J Huntingtons Dis2010; 9: 245–251.
97.
SchultzJLNopoulosPC. Early life functional advantage coupled with accelerated aging: The case for antagonistic pleiotropy in Huntington’s disease. Journal of Huntington's Disease2025: 18796397251391069. doi: https://doi.org/10.1177/18796397251391069
98.
NeemaMSchultzJLLangbehnDR, et al.Mutant huntingtin drives development of an advantageous brain early in life: evidence in support of antagonistic pleiotropy. Ann Neurol2024; 96: 1006–1019.
99.
WaldvogelHJCurtisMABaerK, et al.Immunohistochemical staining of post-mortem adult human brain sections. Nature Protocols2007; 2: 157–169. doi: https://doi.org/10.1038/nprot.2006.354
100.
VonsattelJPGAizawaHDifigliaM, et al.An improved approach to prepare human brains for research. J Neuropathol Exp Neurol1995; 54: 42–56.
101.
TippettLJWaldvogelHJThomasSJ, et al.Striosomes and mood dysfunction in Huntington’s disease. Brain2007; 130: 206–221.
102.
MillerMWKõksSLogueM, et al.Identification of vulnerable cell types in Major brain disorders using single cell transcriptomes and expression weighted cell type enrichment. Front Neurosci2016; 10: 179460.
103.
ZeiselAHochgernerHLönnerbergP, et al.Molecular architecture of the mouse nervous system. Cell2018; 174: 999–1014.e22.
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