Table 1.

Summary of current experimental studies of neuroinflammation in secondary neurodegeneration.

	Strain /Species	Stroke Model	Time Points Post-Stroke	Key Findings
Ross & Ebner, 1990 [182]	Female BALB/c mice	--Ablation of the somatosensory cortex --Intracortical injection of kainic acid	1–120 Days	-2 days after either injury type, astrocytes in the thalamus became reactive and expressed increased levels of GFAP, preceded neuronal loss neurons by at least 2 days following cortical ablation and by 7–10 days following intracortical kainic acid injection -Astrocytes remained reactive up to 60 days after cortical injury.
Herrera & Cuello, 1992 [192]	Male WR	Terminal pia-arachnoid vessel occlusion	1, 4, 7, 15 and 30 Days	-Increase in GFAP+ astrocytes in the thalamus evident from day 4, persisted to 30 days after devascularization. -Correlation between signs of neuronal degeneration and increased GFAP
Morioka, Kalehua & Streit, 1993 [177]	Male WR	Bipolar Coagulation (MCAo)	20 Minutes 3, 6, 18 Hours 1, 2, 3, 5, 7, 14, 21, 28 Days 5, 6, 7 Weeks	-Early microglial activation in contralateral cortex and hippocampus; present and prominent in the thalamus at 2 days, subsided after max intensity reached at 7 days.
Acarin et al., 1999 [193]	Female and Male SDR	Injection of N-methyl-d-aspartate into the right sensorimotor cortex	4 h, 10 h, 1, 3, 5, 7, 14 and 30 Days	-GFAP immunostaining first evident in the thalamus at day 1, peaked at days 3 and 5, resolved by day 14 -Astrocytic response was different in infarct core with the maximum GFAP staining seen at day 7 post-stroke, persisted at 30 days post-stroke.
Dihne & Blocak, 2001 [194]	Male SDR	Transient MCAo	1, 3, 7 and 14 Days	-Microglial activation and increased IL-6 levels in the SN at 3 and 7 days -Reactive astrocytes at 7 and 14 days -Neuronal loss first apparent at 3 days
Zhao et al., 2001 [195]	Male SDR	Permanent MCAo	1, 4, 7 and 12 Days	-Ipsilateral SN neuronal loss peaked at day 4, continued up to day 12 -Increase in reactive astrocytes in ipsilateral SN on days 4 and 7
Dihne et al., 2002 [185]	Male SDR	--Transient MCAo --Photothrombotic	1, 3, 7, and 14 days	-Significant neuronal loss in VPN and RTN following MCAo -GFAP immunoreactivity seen in VPN and RTN at day 1 following MCAo, no significance was noted on day 3, 7 or 14. Similar time course seen in the PT model. -3 days after MCAo activated microglial cells were observed in the VPN and RTN and remained elevated out to 7 and 14 days. Similar time course seen in the PT model -14 days after PT stroke, neuronal loss in the ipsilateral VPN; ipsilateral RTN displayed no signs of neuronal damage
Zhao et al., 2002 [196]	Male SDR	Permanent MCAo	1, 2, 4, 7 and 12 Days	-Increase in reactive astrocytes in the ipsilateral SN, on days 4, 7 and 12
Loos, Dihne & Block, 2003 [197]	Male SDR	Transient MCAo	1, 3 and 7 Days	-Increased TNF-α levels in ipsilateral thalamus at 1 day and SN at 3 days -Activated microglia and astrocytes in the thalamus and SN after 3 days. -Co-localisation of GFAP and TNF-α observed in the thalamus. Co-localisation of NeuN and TNF-α was observed in the SN.
Schroeter et al., 2006 [198]	Wild type and OPN KO mice	Photothrombotic	3, 7 and 14 Days	-Thalamic microglial activation was first apparent at day 7 in both groups. -At day 14, thalamic microglial activation was strongly exacerbated in OPN KO mice. -Neuronal loss in the ipsilateral thalamus, showed no difference between WT and KO mice at day 7, but was greatly exacerbated in KO animals at day 14. -Increased iNOS, IL-1β and TNF-α levels in KO mice at day 1, most pronounced at day 10 -Delayed treatment of OPN KO mice with iNOS inhibitors reduced thalamic neurodegeneration
Justicia et al., 2008 [51]	Male WR	Transient MCAo	MR: 1–7, 10, 14, 20, and 24 weeks IHC: 3, 7, and 24 weeks	-Thalamic T2 hyperintensity detected at 3 weeks after stroke, disappeared around week 7 when T2*-weighted images showed a marked hypointensity in that area. -Neuronal loss was evident in VPL and VPM at 3 weeks, remained out to 24 weeks -Astrocytic and microglial reactivity was first apparent in the thalamus at 3 days -Astrocytic reaction was localized mainly around the VPL and VPM at 7- and 24-weeks post-stroke, forming an astrocytic scar. -Microglial reactivity increased at 7 weeks (compared to 3 weeks), remained elevated at 24 weeks post-stroke. -Reactive microglia in the thalamus showed intracellular iron content at 3 weeks, by 7 weeks the iron showed a parenchymal distribution. After 6 months iron was localized around thalamic structures like Aβ plaques. -APP expression was localized as small dots in the VPL and VPM at 3 weeks, still apparent at 7- and 24-weeks -High density of microglial cells around the APP deposits.
Lipsanen, Hiltunen & Jolkkonen, 2011 [180]	Male WR (Ibuprofen-treated MCAo, MCAo, Sham)	Intraluminal filament model of MCAo	29 Days	-Both astrocytic and microglial activation increased in the ipsilateral thalamus of both MCAo groups compared to shams. Ibuprofen-treated rats showed increased microglial activation compared to MCAo. -Aβ deposits in the thalamus were increased in MCAo animals compared to shams; No differences were seen in the ibuprofen-treated rats compared to MCAo. -Increase of calcium staining was seen in the thalamus in MCAo groups compared to shams. -Significant overall MCAo group effect was seen in limb-placing, beam-walking and cylinder tests when compared to shams; No differences between MCAo and ibuprofen-treated rats.
Jiao et al., 2011 [199]	Male WR	Transient MCAo	3, 7 and 30 Days	-Neuronal loss within ipsilateral hippocampus was increased at all time-points -Treatment with Edaravone decreased the hippocampal neuronal loss. -Increased levels of IL-1β, TNF-α and GFAP+ cells in the ipsilateral hippocampus at day 3 and 7 post-stroke; Treatment with Edaravone decreased these levels. -Edaravone reduced cognitive dysfunction (Water maze task).
Rodriguez-Grande et al., 2013	Male C57/BL6 mice	Transient MCAo	4 and 24 h 6 Days	-Loss of SP in ipsilateral SN at 24 h -Increased number of GFAP+ astrocytes and CD45+ microglia in area of SP loss 24 h. -Neuronal death not observed until 6 days
Walberer et al., 2014 [174]	Male WR	Intra-arterial injection of 2 TiO2 spheres (MCAo)	7 Days and 7 Months	-Ipsilateral thalamus of all animals showed a marked hypointensity in T2*-weighted MRI, indicating iron deposition at 7 months. -Iron deposition localized in and around the phagocytic cells. -Microglia/macrophage activity restricted to the thalamus 7 months post-stroke. -High density of activated microglia/macrophages in the thalamus at 7 months; associated with a loss of NeuN+ neuronal cells and amyloid deposition. -In ipsilateral thalamus, no changes in FDG transport could be observed, thereby indicating normal tissue perfusion.
Patience et al., 2015 [181]	Male C57B/6 mice	Photothrombotic	28 Days	-Significantly increased GFAP expression in the ipsilateral and contralateral hippocampus (CA1, CA2 and CA3), hypothalamus and thalamus at 28 days
Jones et al., 2015 [200]	Male C57BL/6 mice	Photothrombotic	28 Days	-Numbers of microglial-like cells, as well as markers of microglial structural reorganization (Iba-1), complement processing (CD11b), phagocytosis (CD68), and antigen presentation (MHC-II) were all elevated in the thalamus at 28 days and were associated with neuronal loss -Stroke animals that were also exposed to chronic stress exhibited significantly lower levels of microglia and a reduced expression of CD11b in the thalamus compared to the stroke group.
Weishaupt et al., 2016 [179]	Male SDR	Injection of endothelin-1 to induce stroke in the PFC	28 Days	-Post stroke, the DMN of the thalamus, the RSA of the cortex and the IC displayed degenerating cells. -No difference was observed in NeuN+ neurons in the thalamus between stroke and controls. -Area of Iba-1 positive signal in DMN was doubled post-stroke. -Significant neuronal loss and Iba-1 positive cells in RSA post-stroke. -Area of Iba-1 signal in IC significantly higher post-stroke. -No indication of myelin loss in the IC post-stroke.
Cao et al., 2017 [201]	Male C57BL/6 mice	Transient MCAo	30 Days	-Hypothermia initiated at 3.5 hours after stroke reduced primary cortical injury and secondary thalamic injury. -Hypothermia led to a smaller thalamic lesion size, decreased neuronal loss and astrogliosis in the thalamus and less thalamic fibre loss, as well as improvement in functional outcome
Kluge et al., 2017 [202]	Male HCM	Photothrombotic	14 Days	-Microglial process extension lost within the thalamus but remained intact within the lesion site. -Microglia at both sites displayed an activated morphology and elevated levels of activation markers. -Identification of a non-responsive microglia phenotype specific to areas of SND post-stroke.
Anttila et al., 2018 [203]	Male SDR	Transient MCAo	2, 7, 14, 28 and 112 Days	-Activated microglia seen in ipsilateral thalamus at day 7 post-stroke, CD68 immunoreactivity peaked at 14–28 days and persisted until day 112 -Neuronal loss in the ipsilateral thalamus at 14 days -Thalamic astrogliosis seen from day 7 onward, persisted for up to 112 days -(+)-naloxone treatment prevented delayed neuronal death and reduced the number of activated microglial cells in the ipsilateral thalamus and promoted behavioural recovery in the 14-day period.
Jones et al., 2018 [184]	Male HCM	Photothrombotic	14 Days	-PT stroke resulted in increased Iba-1+ cells and reduced NeuN+ cells in the ipsilateral thalamus at 14 days compared to the contralateral thalamus. -Significant numbers of CD4+ and CD8+ T cells detected in ipsilateral thalamus. -Myeloid cells, neutrophils, monocytes, and B cells were not increased in the thalamus post-stroke.
Kluge et al., 2018 [173]	Male HCM	Photothrombotic	3, 7, 14, 28 and 56 Days	-Microglial processes in the thalamus remained responsive to laser-damage for up to 3 days after stroke, at day 7 microglia did not respond to laser damage and this non-responsiveness persisted for up to 56 days; response specific to the thalamus -Impairment of microglial processes extension not due to complete functional paralysis, as continuous engagement in phagocytosis was observed. -Microglial disturbances and neuronal loss appeared to overlap across time and were predominantly located within the Po and VPL. -At days 14, 28 and 56, in the thalamus microglia morphology parameters including cell number, cell area, cell radius, branch length and cell solidity were significantly different to shams.
Kluge et al., 2018 [204]	Young (2–4-month-old) and aged (22–23-month-old) Male C57BL/6J mice	Photothrombotic	7 Days and 28 Days	-Aged mice performed worse in the cylinder task and grid walk task compared to young mice at 7 and 28 days -Levels of synaptic markers in the thalamus were reduced in aged mice compared to young mice at 28 days -Increase in Aβ in the thalamus in aged mice compared to young mice -No differences seen in microglia and astrocytes with age
Ladwig et al., 2018 [205]	Male WR	Photothrombotic	8 Days	-Microglial activation and neuronal loss in thalamus at 8 days, neuronal loss restricted to areas of microglial infiltration. -OPN treatment significantly decreased neurodegeneration, inflammation, and microglial proliferation within the thalamus; no effect on infarct volume. -OPN attenuated the microglial response
Sanchez-Bezanilla et al., 2019 [187]	Male C57BL/6 mice	Photothrombotic	14 Days	-Increased neuronal loss, astrogliosis, Aβ and α-Syn accumulation in the peri-infarct region, thalamus and hippocampus -A loss of AQP4 polarity in the peri-infarct region and thalamus, but there were no significant changes in the hippocampus
Li et al., 2020 [206]	Male wild type C57BL/6 and NLRP10-knockout (KO) mice	Transient MCAo	7, 14 and 28 Days	-Following NLRP10 knockout, levels of microglia and astrocytes in the ipsilateral hippocampus were decreased compared to stroke animals. Motor deficiencies were also relieved post-stroke. -Serum derived from NLRP10-KO mice produced significantly lower concentrations of IL-6, IL-1β and TNF-α. -Significant increase of inflammatory regulators, including IL-6, IL-1β, IL-18, TNF-α, and CD68 in hippocampus; significantly decreased by NLRP10 knockout.
Cao et al., 2021 [207]	Male C57BL/6 mice	Permanent MCAo	1, 3, 7, 14, 28, 56, and 84 Days	-Neuronal loss seen in the ipsilateral thalamus up to 84 days -A unique subtype of CD11c-positive microglia was noted in the thalamus at 28 days. Using flow cytometry, the microglia was shown to have a reduced expression of Tmem119 and CX3CR1, and increased expression of ApoE, Axl, LpL, CSF1, and Cst7
Kim et al., 2021 [190]	Young (11–14 weeks) and aged (18–22 months) male C57BL/6J	Permanent MCAo	3 and 14 Days 6 Weeks 2 Years	-Increase in microglia and astrocytes within the thalamus at day 3, increased at day 14 when neuronal loss was first noted -Aged mice demonstrated reduced microgliosis and astrogliosis compared with young mice -Astrogliosis in the ipsilateral thalamus at 6 weeks post-stroke was similar to that at day 14, but by 2 years had glial scar properties
Sanchez-Bezanilla et al., 2021 [101]	Male C57BL/6 mice	Photothrombotic	7, 28 and 84 Days	-Persistent impairment in cognitive function post-stroke as measured by the PAL and VDR tasks -Neuronal loss and Aβ accumulation seen in the peri-infarct region up to 84 days post-stroke -Levels of inflammatory cells in the peri-infarct region peaked at 7 days post-stroke -Persistent neuronal loss, increased inflammatory cells and Aβ accumulation in the hippocampus up to 84 days post-stroke

Wistar rats (WR), Sprague-Dawley rats (SDR), Heterozygous Cx3CR1GFP/WT mice (HCM), middle cerebral artery occlusion (MCAo), blood-brain barrier (BBB), Osteopontin (OPN), dorsomedial nucleus (DMN), retrosplenial area (RSA), internal capsule (IC), posterior complex (Po), ventral posterior nucleus (VPN), reticular thalamic nucleus (RTN), substantia nigra (SN), ventral posteromedial nucleus (VPM), substance P (SP), paired associates learning (PAL), visual discrimination reversal (VDR) and ventral posterolateral nucleus (VPL).