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DGC_Cck_to_Malat1_BehaviouralAxis.Rmd
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DGC_Cck_to_Malat1_BehaviouralAxis.Rmd
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---
title: "COmponents Readings"
author: "Angus Campbell"
date: "20/03/2022"
output: html_document
---
Definately worht reading:
https://onlinelibrary.wiley.com/doi/full/10.1111/jne.13072
Viho, Eva MG, et al. "Cell type specificity of glucocorticoid signaling in the adult mouse hippocampus." Journal of neuroendocrinology 34.2 (2022): e13072.
-compilation of publicly available scRNA-seq data focusing on GC expression, could be useful for characterizing the other
end of the PC
Fang, R., Xia, C., Close, J. L., Zhang, M., He, J., Huang, Z., ... & Zhuang, X. (2022). Conservation and divergence of cortical cell organization in human and mouse revealed by MERFISH. Science, 377(6601), 56-62.
https://www.science.org/doi/full/10.1126/science.abm1741
-spatial map of gene expression, could be useful for discerning if "reactivation" is really just
differential spatial recruitment
Carazo-Arias, E., Nguyen, P. T., Kass, M., Jee, H. J., Nautiyal, K. M., Magalong, V., ... & Hen, R. (2022). Contribution of the opioid system to the antidepressant effects of fluoxetine. Biological Psychiatry, 92(12), 952-963.
-intorduction has good description of various low trhougput and knowck out studies demonstrating the importance of various opioid receptors in the dnetate gyrus and their suppression of anxiety and depressive behaviour
- they used Habib for thier single cell
These PC's are from the full gene list of the Hochgerner post natal day P35.
PC_ 1
Positive: Malat1, Tmsb10, Rgs4, Sh3bgrl3, Igfbp6, Rasgrp1, Chgb, Nptx2, Penk, Inhba
Sgk1, Rprm, Prkcdbp, Nefm, Ier5, Aldoa, Nefl, Scn1b, Lingo1, Shisa4
Aldh3b1, Snhg11, Kcnk1, Bdnf, Ppp1r1a, Arpp21, Gsg1l, Tesc, Meg3, Chchd10
Rbp4, Syne1, Srxn1, Ddit3, Myh14, Kcnip3, Necab3, Gpr83, Fbxo32, Serpine2
Tpt1, Vgf, Scg5, S100a6, Plk2, Ttyh1, Zfp804a, Sult2b1, C1ql2, Hsph1
Negative: Tmsb4x, Cck, Ahcyl2, Snca, Tubb2b, Olfm1, Pgm2l1, Neurod2, Adcyap1r1, Igfbp5
Nsg2, Mpc2, Crym, Capn3, Rplp0, Tubgcp2, Ddn, Frzb, Rogdi, Nt5dc2
Ccdc28b, Plppr4, Ly6h, Wbp11, Faim, Prrt1, Tpd52l1, Nsmf, Rnf165, Nme1
Trim2, Spns2, Inf2, Eif1b, Pde1a, mt-Nd1, Elfn2, Limd2, Fam213a, Gfra1
Gm13889, Spock2, Sipa1l2, Nrp1, Bhlhe22, Mfap3, Nnat, Gm10605, Syce2, Tmem114
PC_ 2
Positive: Aldoa, Inhba, Rgs4, Rprm, Zwint, Lingo1, Meg3, Grp, 1110008P14Rik, Penk
Mlf2, Ap1s1, Arpp21, Snca, Nptxr, Chgb, Resp18, Shisa4, C1ql2, Bdnf
Krt2, Klc1, Aldh3b1, Snhg11, Tpt1, Hint1, Gm10605, Synpo, Gng3, Plk2
Clta, Hsph1, Trim32, Xbp1, Scn1b, Ttc3, Ddit4l, Srxn1, Cmip, Nptx2
Syn2, Rtn4rl1, 0610012G03Rik, Nptx1, Mrpl30, Sh3bgrl3, Ppp1r1a, Tspan7, Gsg1l, Nefl
Negative: Malat1, Ahcyl2, Actb, Tmsb4x, Ppm1h, Fst, Nat8l, Epha5, Neurod2, Dsp
Ccdc28b, Gm13889, Adcy1, Inf2, Opcml, Ptpn9, Sox4, Cep95, Ythdf2, Fchsd2
Dpagt1, Rccd1, Ubiad1, Snapc4, Zbtb34, Pls3, Il16, Bhlhe22, Tmem8b, Il18
Slc4a4, Gse1, Sdccag8, Lrp8, Mterf1b, Tpcn1, Clptm1, Rint1, E130308A19Rik, Jph1
Chrna1os, Scaf11, Wdr12, Bbc3, Tbl3, Snap29, Rnf19b, Klhl20, Cars, Wbscr25
PC_ 3
Positive: Tmsb10, Eif4a2, Fxyd6, Junb, Aldoa, Jun, Grp, Tuba1a, Gng3, Cxcl12
Scg5, Nap1l5, Tagln3, Mff, Cisd1, Snca, Fxyd7, Ppp3r1, Rsrp1, Zwint
Polr2m, Nsg1, Rpl15, C1ql2, Tprgl, Ier2, Wbp5, Ephx4, Ahi1, Necab3
Cited2, Vapa, Hint1, Tmem50a, Arl4a, 1500011B03Rik, Atp6v1f, Nrsn1, Bex1, Nme1
Pafah1b3, Dap3, 2610524H06Rik, Mia, Smim10l1, Snhg11, Eif4h, 3110082I17Rik, Pkia, Lamtor5
Negative: Inhba, Epha10, Adcy1, Asb11, Arc, Lingo1, Ddn, Nptx2, Chst1, Trim2
Kcnf1, Adgrb1, Rasd1, Wipf3, Syne1, Dclk1, Samd4, Pgbd5, Pdgfb, Cyfip2
Srxn1, Cenpa, Actb, Atp1b1, Pmepa1, Rasgrf1, Ptn, Lgi1, Baz1a, Ppm1l
Gadd45b, Adgrl1, Hist1h2bc, Dlg3, Ahcyl2, Synpo, Ntrk3, Efhd2, Nefm, Smad7
Inf2, Midn, Mt1, Neurod2, Tanc1, mt-Nd1, Prpf38b, Pcdh8, Lrp12, Kcnj4
PC_ 4
Positive: Snhg11, Meg3, Krt2, Gm10605, Grp, Rprm, Tenm4, Tenm2, Pde1a, Arpp21
Akap5, Ttyh1, Fam65b, Faim, Mycbp2, Icam5, Shisa4, Nsg2, Resp18, Timp2
Lmo4, Lpin2, Cbx6, Kcnq1ot1, Ngb, Arrb1, Scg2, Prune2, Nptxr, Ptpra
Ctsb, Mpped2, Ttc3, Penk, Igfbp6, Tmeff2, Syn2, Pgm2l1, Atpaf1, Aldh3b1
Nbea, Unc5a, Ep400, Mier1, Faf2, Gpd2, Megf8, Iqgap2, Dtx4, Mapk8ip1
Negative: Tmsb4x, Ier2, Gadd45b, Junb, Arc, Rheb, Inhba, Samd4, Cenpa, Gadd45g
Midn, Hist4h4, Fos, Tuba1a, March11, Asb11, Rasd1, Tagln3, Bex2, Baz1a
Srsf5, Aldoa, Efhd2, Kcnf1, Pcdh8, Smad7, Psmb2, Jun, Ybx1, Homer1
Fxyd7, Tpd52l2, Cltb, Nefl, Ppp1cb, Vapa, Cdc42, Dclk1, Csnk1a1, Plk2
Park7, Nr4a1, Pabpc4, Eef2, Ube2d3, Epha7, Synpo, Nme1, Nptx2, Vgf
PC_ 5
Positive: Timp2, Meg3, Grp, Midn, Junb, Nrp1, Fxyd7, Vgf, Gng3, Arc
Gadd45g, Ly6h, Gadd45b, Nnat, Lingo1, Pdgfb, Tenm4, Mia, Egr1, Inhba
Crym, Bcl2, Gm16062, Basp1, Wdr6, Fxyd6, Nr4a1, mt-Nd1, Tmem158, Samd4
Resp18, Kcnq1ot1, Spns2, Rasd1, Spock2, Sec22a, Cck, Cenpa, Bdnf, Qsox1
March11, Ptpre, Rwdd3, Snhg11, Tmsb10, Pithd1, Baz1a, Cntnap2, Rtn4rl1, Synpo
Negative: Ppp1r1a, Hist1h2bc, Adcy1, Opcml, Eif4a2, Epha5, Stk32c, Chn1, Fam101b, Neurod2
Park7, Ddn, Ppp3r1, Ppp1r9a, Epha7, Rasgrp1, Sh3bgr, Igfbp6, Tpgs1, Wbp11
Iqgap2, Aamdc, Limd2, Map7d1, Mat2b, Rccd1, Rgl1, Kars, Ndrg4, Mmp17
Psmb5, Minos1, Gng2, Eef2, Arpc1a, Nufip1, Sat2, Dsp, 1500011B03Rik, Rprm
Ddit4l, Arpc5, Igbp1, Pgbd5, Csdc2, Xlr3b, C1qbp, Poldip2, Mrps23, Chchd10
PC_ 6
Positive: Snca, Rplp0, Agap1, Ccnl2, Usp22, Pgm2l1, Mical2, Aldh3b1, Pgbd5, Ncs1
Dnlz, Sec61b, Eif4a2, Rabac1, Gxylt2, Synpo, Mpp1, Evl, Rnf32, Wdr19
Apoe, Atxn7l3b, Dlg3, Cygb, Prrt1, Rpl7a, Dennd4a, Larp7, Elavl3, Sh3d19
Rpl15, Ppp1r1a, Nptx1, Rab36, Wasf1, Trappc2l, Stau2, Fam188a, Drd4, Kcnj3
Galt, Etnk2, Ankrd26, Nvl, Tmem8b, Ctdsp2, Nit2, Sap30, Rala, Zfp81
Negative: Junb, Scg5, Faf2, Fos, Ier2, Btg2, C2cd4b, Zfp956, Lrp11, Tmem246
Gde1, Derl1, Egr1, Serpine2, Gadd45g, Mtor, Cpox, Usp36, Nap1l4, G6pc3
Vmp1, Mpc2, Slc2a6, Gm26802, Ghitm, Cabp1, Fam65b, Cisd1, Fam213a, Gm13889
Hist4h4, Telo2, Atp6v1d, Sipa1l2, Nrn1, Prkd2, Polrmt, Nsg2, Man2c1, Vegfb
Cttn, Jun, Fam214b, Zfp112, Tsc22d1, Tm2d1, Tmem240, Uchl3, Cited2, Ly6h
Environmental Enrichment effects on DG expression (bulk I think)
https://www.frontiersin.org/articles/10.3389/fnmol.2018.00126/full
From PC1:
Cck Loading:
Crym
Lamia, K. A., Papp, S. J., Yu, R. T., Barish, G. D., Uhlenhaut, N. H., Jonker, J. W., ... & Evans, R. M. (2011). Cryptochromes mediate rhythmic repression of the glucocorticoid receptor. Nature, 480(7378), 552-556.
-the fact this is expressed in the more inactive branch could indicate mice are not expressing this
Cck
Flati, T., Gioiosa, S., Chillemi, G., Mele, A., Oliverio, A., Mannironi, C., ... & Castrignanò, T. (2020). A gene expression atlas for different kinds of stress in the mouse brain. Scientific Data, 7(1), 1-18.
-Cck shows up across many tissues
https://www.biorxiv.org/content/10.1101/2021.09.25.461769v2.full
Desai, A. J., Dong, M., Harikumar, K. G., & Miller, L. J. (2016). Cholecystokinin-induced satiety, a key gut servomechanism that is affected by the membrane microenvironment of this receptor. International journal of obesity supplements, 6(1), S22-S27.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5485878/
-Cck is a short acting satiety inducing hormone and the DG cells are producing it
Longitudinal Axis
Levone, B. R., Moloney, G. M., Cryan, J. F., & O'Leary, O. F. (2021). Specific sub-regions along the longitudinal axis of the hippocampus mediate antidepressant-like behavioral effects. Neurobiology of stress, 14, 100331.
Anacker, C., Luna, V. M., Stevens, G. S., Millette, A., Shores, R., Jimenez, J. C., ... & Hen, R. (2018). Hippocampal neurogenesis confers stress resilience by inhibiting the ventral dentate gyrus. Nature, 559(7712), 98-102.
Fear Behaviour Natural Behaviour studies:
https://www.nature.com/articles/s41539-017-0007-4
https://www.sciencedirect.com/science/article/pii/S0896627319304775#bib77
Lozano-Montes, L., Dimanico, M., Mazloum, R., Li, W., Nair, J., Kintscher, M., ... & Rainer, G. (2020). Optogenetic stimulation of basal forebrain parvalbumin neurons activates the default mode network and associated behaviors. Cell Reports, 33(6), 108359.
https://www.sciencedirect.com/science/article/pii/S2211124720313486
Here study confirms penk is highly localized:
Johnston, H. M., & Morris, B. J. (1994). Induction of c-fos gene expression is not responsible for increased proenkephalin mRNA levels in the hippocampal dentate gyrus following NMDA stimulation. Molecular brain research, 25(1-2), 147-150.
Penk in CA2 VIP interneurons inportant for social memory
https://www.nature.com/articles/s41380-021-01124-y#Sec2
Ca2+ imaging of CA2 shows odor specific topography
Hassan, S. I., Bigler, S., & Siegelbaum, S. A. (2021). Coding of social odors in the hippocampal CA2 region as a substrate for social memory. bioRxiv.
Jarzebowski, P., Hay, Y. A., Grewe, B. F., & Paulsen, O. (2022). Different encoding of reward location in dorsal and intermediate hippocampus. Current Biology.
-publications of tetrode
-pdf of entire thesis is in SteinmetzLab fodler on PC
FROM ICA OF THE ENGRAM DEGs
IC_ 1
Positive: Rps14, Rps18, Pcdh20, Rpl17, Fam19a1, Rpl10, Rpl4, Arhgap44, Asns, Set
P4ha1, Crtac1, Rasa3, Rpl7, Rpl36al, Agpat4, Ric8, Pcgf2, Gm26981, Cacna1a
Ptma, Eif3l, Ppp1r8, Hnrnpa1, Kdm5a, Gpbp1, Brap, Mlip, Coro1a, Rgs17
Negative: Gadd45b, Inhba, Rasd1, Asb11, Arc, Npas4, Baz1a, Acan, Nptx2, Kcnf1
Samd4, Midn, Iqsec3, Rasl11b, Atf3, Csrnp1, Smad7, Sertad1, Osgin2, Fosl2
Lingo1, Zfp655, Plk2, Fosb, Fgfr1, Elmo1, Nr4a1, Neat1, Numbl, Srxn1
IC_ 2
Positive: Hs3st1, Prex1, Per2, Rasd1, Sec24a, Atxn7, Pdia6, Chga, Epha10, Pxmp4
Tbk1, Pcnx, Lrfn2, Rpn1, Il1r1, Smyd4, Galnt9, Clstn3, Slc25a36, Mirg
Nrp1, Pde4a, Usp14, Dusp4, Calr, Klhl32, Pak6, Gprasp1, Bdnf, Ssr2
Negative: Rps14, Rpl41, Aldoa, Rpl19, Rpl10, Rps11, Oaz1, Rpl4, Rpl21, Eif5a
Rpl17, Timm13, Rps18, Rplp0, Pfn1, Ybx1, Atp5d, Clta, Cct5, Rpl7
Ensa, Eef2, Cox14, Rpsa, Ptma, Smim14, Hnrnpk, Eif4a1, Zwint, Amd1
IC_ 3
Positive: Klhl40, Drd4, Npy, Kcnj2, Rgs4, Unc13d, Ttyh1, Chgb, Gsg1l, Cdkn1a
Frmd6, Rnh1, Batf3, Arc, Rtn4rl1, Tmod1, Svil, Daglb, Pde4d, Slc6a8
Trnp1, Dot1l, Sv2c, Dcdc2a, Shisa4, Gm4208, Plk2, Ice1, Atp6v1b2, Glcci1
Negative: Smad7, Oaz1, Rangap1, Eif3l, Coro2b, Cnppd1, Zbtb1, Entpd7, Pja1, Fosb
Nrp1, Med13, Ptma, Cystm1, Snap91, Snf8, Mrpl44, Pdia6, Pde4a, Gm13889
Churc1, Dmxl1, Mat2a, Hax1, Ranbp2, Sec63, Clstn3, Sbds, Gid8, St7
IC_ 4
Positive: Amd1, Sox11, Arxes1, Fbxo33, Ggnbp2, Spsb1, Smim13, Cdkn1a, Myh9, Micu1
Gm4208, Churc1, Errfi1, Dpysl5, Tdrd7, Tulp3, Nab2, Lrtm2, Hspa14, Ensa
Rasl11a, Slc41a1, Gabrb1, Spns2, Rrp1b, Erh, Tmem35, Csde1, Lrfn2, Bzw1
Negative: Asb11, Megf11, Neat1, Daglb, Cenpa, Prpf38b, Drd4, Dgki, Dhps, Lingo1
Efhd2, Nefm, Bhlhe41, Nifk, Blnk, Mrpl44, Dtna, Cntn3, Iqsec3, Sec63
Hsf2, Tufm, Gm27004, Trank1, Rbbp7, Cystm1, Tpt1, Rapgef6, Dock3, Rgs4
IC_ 5
Positive: Lrfn2, Ncs1, Srebf2, Snx1, Osbpl6, Ano6, Oaz1, Ascc3, Trpm2, Abr
Ppm1h, Sema3e, Pip5k1a, Kdm5a, Nrp2, Acvr1c, Csnk2a1, Prorsd1, Mgat4a, Zfc3h1
Scg2, Stx1b, Meg3, Ppp1r16b, B830012L14Rik, Camta2, Ildr2, Prickle2, Klhl32, Cntn5
Negative: Ssr2, Sf3b1, Pja1, Arpc2, Stmn4, Ddx24, Cfl1, Cap1, Zc3h15, Hnrnpk
Rpl7, Rab11a, Slc6a6, Ssr1, Snf8, Commd7, Ensa, Gm16286, Sgta, Kcnk1
Nop56, Eif4a1, Mphosph8, Stip1, Hnrnpll, Efhd2, Eif5a, Arxes1, Ric8, Hsp90aa1
In IC_1 NOTE THAT THIS IS RUN SPECIFICALLY ON THE JEAGER ET AL. GENEs
https://www.nature.com/articles/npp20114
-opiod receptors in amny brain regions are subject to expression changes in response
to various diets
Chang, S., Bok, P., Tsai, C. Y., Sun, C. P., Liu, H., Deussing, J. M., & Huang, G. J. (2018). NPTX2 is a key component in the regulation of anxiety. Neuropsychopharmacology, 43(9), 1943-1953.
-Npt2x supresses anxiety
Pinzari, C. A., Kang, L., Michalak, P., Jermiin, L. S., Price, D. K., & Bonaccorso, F. J. (2020). Analysis of genomic sequence data reveals the origin and evolutionary separation of Hawaiian hoary bat populations. Genome biology and evolution, 12(9), 1504-1514.
BAZ1A is mutated in bat populations showing differences in foragin behaviours
Conith, M. R., Hu, Y., Conith, A. J., Maginnis, M. A., Webb, J. F., & Albertson, R. C. (2018). Genetic and developmental origins of a unique foraging adaptation in a Lake Malawi cichlid genus. Proceedings of the National Academy of Sciences, 115(27), 7063-7068.
-smad4 is mutated in a fish species with different foragin behaviours, it was implicated with snout shape in this study which
is useful for certain behaviours
Wang, C. N., Gong, S. N., Guan, W., Wang, J. L., Gao, T. T., Wang, Y., ... & Jiang, B. (2020). Hippocampal overexpression of chordin protects against the chronic social defeat stress-induced depressive-like effects in mice. Brain research bulletin, 158, 31-39.
-smad4 suppresses stress
Krampert, M., Chirasani, S. R., Wachs, F. P., Aigner, R., Bogdahn, U., Yingling, J. M., ... & Heuchel, R. (2010). Smad7 regulates the adult neural stem/progenitor cell pool in a transforming growth factor β-and bone morphogenetic protein-independent manner. Molecular and cellular biology, 30(14), 3685-3694.
-smad7 also appears to regulate neurogenesis in the dentate gyurs
Faguet, J. (2014). The role of neuropeptide signaling in C. elegans food sensation and social behavior. University of California, San Francisco.
-in celegans smad is assocaited with foraging, in food rich environments
Fear memories are not replayed during theta osscilations: Feng, H., Su, J., Fang, W., Chen, X., & He, J. (2021). The entorhinal cortex modulates trace fear memory formation and neuroplasticity in the lateral amygdala via cholecystokinin. bioRxiv.
-Cck -/- mice display lower freezing behaviour in conditioned fear task,
tasks were either given with short or long trace tasks, where tone predciting shock was played either 2s or 10s respesctively
before shock, to investigate Hp ability to assocaite events occuring over long periods of time
-scaring the mice with white noise does and measuring immediate fear responses show no difference between wild type and regular mice, suggesting the
Cck is expressed in fear memories in entorhinal cortex in neurons that project to Cck expressing neurons in amygdala,
this circuit is likely driving fear memory formation
Feng, H., Su, J., Fang, W., Chen, X., & He, J. (2021). The entorhinal cortex modulates trace fear memory formation and neuroplasticity in the mouse lateral amygdala via cholecystokinin. Elife, 10, e69333.
Smagin, D. A., Kovalenko, I. L., Galyamina, A. G., Bragin, A. O., Orlov, Y. L., & Kudryavtseva, N. N. (2016). Dysfunction in ribosomal gene expression in the hypothalamus and hippocampus following chronic social defeat stress in male mice as revealed by RNA-Seq. Neural Plasticity, 2016.
Rpl7 is implicated in chronic social stress in rodents
-RNA seq study
Sagehashi, N., Obara, Y., Maruyama, O., Nakagawa, T., Hosoi, T., & Ishii, K. (2022). Insulin enhances gene expression of Midnolin, a novel genetic risk factor for Parkinson's disease, via ERK, PI3-kinase and multiple transcription factors in SH-SY5Y cells. Journal of Pharmacology and Experimental Therapeutics.
-Midn is expressede in response to insulin
Barbier, M., Chometton, S., Pautrat, A., Miguet-Alfonsi, C., Datiche, F., Gascuel, J., ... & Risold, P. Y. (2020). A basal ganglia-like cortical–amygdalar–hypothalamic network mediates feeding behavior. Proceedings of the National Academy of Sciences, 117(27), 15967-15976.
-a basal ganglia like feeding network exists between cortex, amygdala and hypothalamus and may have split from the basal ganglia
Flati, T., Gioiosa, S., Chillemi, G., Mele, A., Oliverio, A., Mannironi, C., ... & Castrignanò, T. (2020). A gene expression atlas for different kinds of stress in the mouse brain. Scientific Data, 7(1), 1-18.
-visual cortex, dentate gyrus and other regions have elevated Cck expression in stress conditions
REASOURCES:
Cell atlas for testing conservation of cell types
https://www.cell.com/cell-reports/pdf/S2211-1247(21)00117-0.pdf
-likely insufficiently detailed view of dentate gyrus to know if the expression is conserved
Schmitz, M. T., Sandoval, K., Chen, C. P., Mostajo-Radji, M. A., Seeley, W. W., Nowakowski, T. J., ... & Pollen, A. A. (2022). The development and evolution of inhibitory neurons in primate cerebrum. Nature, 1-7.
-Evolution of various inhibitory cell types
-200k+ cells used from multiuple species and multiple regions
Krienen, F., Goldman, M., Mullally, C., Reed, N., McCarroll, S., & Berretta, S. (2021). A Cell Atlas of the Human Amygdala. Biological Psychiatry, 89(9), S11-S12.
-human cell types of the amygdala with comparisson to mouse and marmoset may be useful
Wang, W., Wang, M., Yang, M., Zeng, B., Qiu, W., Ma, Q., ... & Wang, X. (2022). Transcriptome dynamics of hippocampal neurogenesis in macaques across the lifespan and aged humans. Cell Research, 32(8), 729-743.
https://www.nature.com/articles/s41422-022-00678-y#Sec11
-single nucleaus of macaque and human