The protocol describes methods to study micromorphological changes in neurons and the transition of mitochondrial cytochrome c by immuno-transmission electron microscopy.
Method Article
* These authors contributed equally
The protocol describes methods to study micromorphological changes in neurons and the transition of mitochondrial cytochrome c by immuno-transmission electron microscopy.
Protein location changes in the microstructure often present a precise regulation mechanism at the level of pathological organelles. How to accurately capture the location of this organelle protein transfer has positive significance and value for the diagnosis and treatment of diseases. Mitochondria play a central role in necrosis and the intrinsic pathway of apoptosis. Under normal conditions, cytochrome c (Cyt c) only exists between the inner and outer membranes of mitochondria and in the nucleus. When cells undergo apoptosis, the mitochondrial inner membrane permeability is altered, and Cyt c is released from mitochondria into the cytoplasm. In this study, a rat model of cerebral ischemia-reperfusion injury was established, and the micromorphological changes of neurons undergoing apoptosis were shown by immuno-transmission electron microscopy. Additionally, it shows the vision of immunogold labeling Cyt c transfer from the mitochondrial matrix to the cytoplasm after cerebral ischemia-reperfusion injury more precisely. The immuno-transmission electron microscopy technique presented in this protocol is suitable for the demonstration of any protein position transitions at the microscopic level.
According to the 2021 global burden of disease study, stroke was the 3rd leading cause of death and the 4th leading cause of disability-adjusted life-years. There were 11.9 million new stroke events, in which ischemic stroke constituted 65.3% (7.8 million)1. Neuronal death occurs after cerebral ischemia, including necrosis and apoptosis. The most severely affected brain tissue subsequently undergoes necrotic cell death. Neurons in the ischemic penumbra or periinfarct zone may undergo apoptosis after several hours or days2. In addition to bioenergetic and metabolic functions, mitochondria also play a central role in the intrinsic pathway of apoptosis3,4,5,6.
Cyt C is a protein encoded by nuclear genes. Under normal conditions, Cyt C only exists between the inner and outer membranes of mitochondria and in the nucleus. The apoptotic pathway mediated by its release is associated with the regulatory control of Bcl-2 family members. After being stimulated by apoptosis, Bax/Bak oligomers are formed and inserted into the mitochondrial outer membrane pore, resulting in changes in mitochondrial osmotic pressure and loss of transmembrane potential. Cyt C is released from mitochondria to the cytoplasm, where it binds to the activator of apoptosis 1 to form the apoptotic complex and activate pro-caspase-9. In turn, caspase-3 and caspase-7 are activated, which initiates the Caspase cascade and induces cell apoptosis7.
Transmission electron microscopy (TEM) can clearly observe the changes in cell structure at different stages of apoptosis. Electron microscopy morphological observation is a reliable method for determining apoptosis8. However, it cannot observe changes in Cyt C in ultrastructure. There are several techniques for detecting specific proteins in ultrastructure: flow cytometry, enzyme-Linked Immunosorbent assay, enzyme-linked immunosorbent assay, spectrophotometry, and Western blotting. However, they cannot accurately capture the location changes of protein in the microstructure. Colloidal gold has particles of different sizes, and the electron density of colloidal gold is high. Immunogold technology is particularly suitable for single or multi-label localization studies of immuno-electron microscopy. Due to its inherent light-to-dark red coloration, colloidal gold is also amenable to observation under light microscopy. When specific proteins are Immunogold labeled, the location changes can be visualized by means of a TEM at a subcellular resolution9.
This protocol describes highlighting the transition of mitochondrial Cyt C by immuno-transmission electron microscopy (IEM). The overall goal of this method is to visualize the subcellular translocation of Cyt C during ischemia-induced apoptosis usingIEM. The rationale for IEM is to label Cyt C with colloidal gold and visualize its localization changes at subcellular resolution using TEM9. IEM can observe the dynamic changes of proteins at the spatial level, providing a powerful means for explaining physiological and pathological activities10.
The animal program has been approved by the Ethical Committee of SLAS (IACUC Issue No: SYST-2024-018). Here, 6 pathogen-free male SD rats (200-220 g) were raised in independent ventilation cages, maintaining the laboratory environment at 22-25 °C and 45%-65% relative humidity. All rats underwent adaptive feeding for 1 week with free water and diet during the period.
1. Establishment of middle cerebral artery occlusion (MCAO) model
2. Restoration of middle cerebral artery blood flow
3. Assessment of neuroscore
4. Brain tissue collection
5. Sham operation
6. Ultrathin section preparation and imaging
7. Immunogold labelling
The neuroscore evaluation confirms the success of MCAO, according to Longa Score Scale, rats in MCAO group presented at least circling to the left (neuroscore 2). Rats of the sham operation group showed no obvious neurological dysfunction (neuroscore 0). No mortality was observed during the surgery day.The animals' neuroscore are listed in Table 1.
IEM analysis of the MCAO group revealed neurons with shrunken nuclei and elevated cytoplasmic electron density, accompanied by partial mitochondrial structural disruption. Critically, the immunogold-labeled Cyt c exhibited a marked redistribution: compared to the sham group's predominant mitochondrial localization, the MCAO samples showed a significant decline in mitochondrial gold particles alongside abundant cytosolic and nuclear labeling. This spatial shift of Cyt c from mitochondria to the cytoplasm and nucleus directly visualizes mitochondrial outer membrane permeabilization and confirms the activation of the intrinsic apoptotic pathway following cerebral ischemia-reperfusion injury. The correlation between these ultrastructural changes and Cyt c translocation provides conclusive evidence of apoptosis initiation at the subcellular level.
TEM showed that the ultrastructure of hippocampal neurons in the sham operation group was normal, and no lesions were observed in mitochondria and endoplasmic reticulum. In the MCAO group, some neurons showed pyknosis and degeneration, showing the characteristics of pre-necrotic changes, mitochondrial swelling or destruction, and endoplasmic reticulum dilation. The results of IEM showed that the colloidal gold particles (mark Cyt C) in the sham-operated group were mainly distributed in the nucleus and mitochondria, and a few were scattered in the cytoplasm. The colloidal gold particles in the MCAO group were less distributed in the mitochondria and were abundant in the endoplasmic reticulum of the cytoplasm. This shows that after cerebral ischemia-reperfusion injury, brain tissues undergo necrotic cell death and apoptosis, and in those processes, Cyt C is released from the mitochondria into the cytoplasm.Mitochondria play a central role in bioenergetic and metabolic functions. Release of Cyt c from mitochondria is a critical checkpoint in cerebral I/R injury, bridging mitochondrial damage to cell death execution12 (Figure 3 and Figure 4).

Figure 1: Experimental flowchart. (A) Brain tissue fixation process. (B)TEM process and IEM process workflow. Please click here to view a larger version of this figure.

Figure 2: Equipment and apparatus used here. (A) Brain tissue collection. (B) Brain tissue fixation process. (C) Ultrathin section preparation. (D) Transmission electron microscopy. Please click here to view a larger version of this figure.

Figure 3: TEM analysis. TEM images of neurons in the sham operation group and MCAO group.In the sham group, neurons show normal ultrastructure: the nuclear membrane (N) is smooth, chromatin is evenly distributed, and the nucleolus is visible. Mitochondria (red arrows) have intact membranes and clear cristae. The rough endoplasmic reticulum (blue arrows) and Golgi apparatus (yellow arrows) are normal. In contrast, neurons in the MCAO group are pyknotic and degenerated, with wrinkled nuclear envelopes and increased electron density. Mitochondria show disrupted cristae, and the rough endoplasmic reticulum and Golgi apparatus are dilated. Abbreviations: N = nucleus; TEM = transmission electron microscopy; MCAO = middle cerebral artery occlusion; IEM = immuno-transmission electron microscopy. Please click here to view a larger version of this figure.

Figure 4: IEM analysis. IEM images showing subcellular localization of gold-labeled proteins. In the sham group, neurons display normal ultrastructure. Colloidal gold particles (black arrows) are found in mitochondria, and others (orange arrows) are distributed in nuclei and cytoplasm. In the MCAO group, neurons show slight shrinkage and increased electron density. Fewer gold particles are present in mitochondria, but more are found in nuclei and cytoplasm. Abbreviations: N = nucleus; TEM = transmission electron microscopy; MCAO = middle cerebral artery occlusion; IEM = immuno-transmission electron microscopy. Please click here to view a larger version of this figure.
| Animal | Neuroscore |
| Sham 1 | 0 |
| Sham 2 | 0 |
| Sham 3 | 0 |
| MCAO 1 | 2 |
| MCAO 2 | 3 |
| MCAO 3 | 2 |
Table 1: Comparison of neuroscore between sham and MCAO groups. p = 0.034. Abbreviations: MCAO = middle cerebral artery occlusion.
The primary objective of reperfusion therapy in acute ischemic stroke is to restore blood perfusion to the ischemic region. Now we can achieve this goal through intravenous thrombolysis, endovascular treatment, and antithrombotic therapy. However, restoration of blood perfusion leads to ischemia-reperfusion injury, aggravates neuronal necrosis and apoptosis, leading to neurological impairment. During ischemia-reperfusion, abnormal leakage of electrons from the mitochondrial electron transport chain leads to the production of a large amount of mitochondrial reactive oxygen species, which damages the mitochondrial membrane and releases Cyt c and mitochondrial DNA13. Studies have demonstrated that Bax channel inhibitors and insulin can activate cell survival signaling, prevent apoptotic release of Cyt c, and exert neuroprotective and antiapoptotic effects14,15.
Immunohistochemistry allows us to visualize and localize specific biochemical components in cell compartments and tissues. Combined with TEM, we can accurately capture the location changes of protein in the microstructure. Immune colloidal gold technique has made great progress in successfully applying to various aspects of cell biology and the study of cellular ultrastructure level of immunology, histology, and pathology16,17,18. It has been used in renal diseases and tumor diagnosis19,20, study of molecular mechanisms of different diseases21,22. Compared with traditional biochemical techniques such as Western blotting, enzyme-linked immunosorbent assay, and immunohistochemistry, IEM has obvious advantages in the ultrastructural precision visualization of subcellular protein localization. Although these traditional methods can detect expression levels, they cannot capture the precise spatial changes in protein distribution. In contrast, IEM can directly observe the redistribution of proteins such as Cyt c from mitochondria to the cytoplasm during apoptosis, providing strong visual evidence to support mechanistic hypotheses. This advantage has been demonstrated in the remaining studies10,23.
Fixation is a critical step in immuno-electron microscopy, as it requires a balance between preserving cellular ultrastructure and maintaining antigenicity. Inadequate fixation may lead to loss of ultrastructural integrity, while overly strong fixatives can mask antigenic sites and reduce labeling efficiency24. In this experiment, special care must be taken when sampling fresh tissue. The sampling site should be carefully selected to avoid mechanical damage such as traction, contusion, or compression. Additionally, the tissue thickness should be kept below 2 mm to ensure optimal fixative penetration and structural preservation.
Although compared to TEM, IEM can capture the changes of mitochondrial proteins in the microscopic structure, such as the changes in the position and quantity of these proteins in the cytoplasm or other organelles, and with the mitochondria. However, IEM only explains certain phenomena from the perspective of mitochondrial morphology and functional proteins. As for the true function of mitochondria, it is necessary to combine the detection of adenosine triphosphate, adenosine diphosphate, and adenosine monophosphate contents using high-performance liquid chromatography or directly detect the functional state of mitochondria through the Seahorse method25,26,27.
There are limitations to this technique; it cannot be used in live cells. Fixatives often exert varying degrees of influence on the activity of antigens; to preserve the ultrastructure of cells and the activity of antigens, it is necessary to determine the type, concentration, temperature, pH, and fixation time and method of the fixative through preliminary experiments. Known-titer antigens can be used for testing to select an appropriate fixation method. There are six rats randomly divided into the MCAO group and the sham operation group, with three in each group. To exclude the effects of anesthesia, surgical trauma, and other confounding factors, we may need more animals and a control group in further study. This group would not undergo any surgical procedures but would receive the same anesthesia and fixation processing, allowing us to distinguish the effects of surgery from those of other experimental manipulation.
This method provides an effective means for the accurate localization of various antigens in the ultrastructure of tissues and cells, also one way to confirm the relationship between cell structure and function and the changes in pathological conditions. We believe this method can be applied to further study of underlying cellular mechanisms involved in different diseases with different disease animal models, including drug discovery.
The authors have nothing to disclose.
This work was supported by the Special Scientific Research Project on Traditional Chinese Medicine of Sichuan Provincial Administration of Traditional Chinese Medicine(2021MS414).
| Name | Company | Catalog Number | Comments |
|---|---|---|---|
| 0.9% normal saline | Sichuan Kelun Pharmaceutical Co., Ltd. | H20083400 | |
| 200 Mesh formvar coated copper grids | Zhongjingkeyi Technology Co., Ltd. | BZ10262a | |
| 220-230g MCAO Monofilaments | Beijing Cinontech Co., Ltd. | A4-243250 | |
| Absolute ethanol | Chengdu Kelong Chemical Co.,Ltd. | 2023101201 | |
| acetone | Chengdu Kelong Chemical Co.,Ltd. | 2023120501 | |
| Animal anesthesia system | Rayward Life Technology Co., Ltd. | R500 | |
| Animal temperature maintainer | Rayward Life Technology Co., Ltd. | 69020 | |
| Baking table | Shenzhen Bangqi Chuangyuan Technology Co., Ltd. | CT-946 | |
| Bone shear | Fine Science Tools | 16102-11 | |
| capsular embedding molds | Zhongjingkeyi Technology Co., Ltd. | GP130-B | |
| Centrifuge | SCILOGEX | D3024R | |
| Conventional bright-field optical microscopy | Zeiss (Germany) | Primo Star | |
| Curved ophthalmic forceps (10 cm) | Shanghai Medical Equipment Co., Ltd. | 211001 | |
| Diamond knife | Diatome (Switzerland) | DU4530 | |
| Dissecting forceps | Rayward Life Technology Co., Ltd. | F12018-10 | |
| Dissecting forceps | Rayward Life Technology Co., Ltd. | F12010-10 | |
| Electric blast drying oven | Shanghai YiHENG Scientific Instrument Co., Ltd. | DHG-9030A | |
| Electric shaver | Yiwu Kemei Electric Appliances Co., Ltd. | KM-PG5002 | |
| Fixation fluid | Sichuan Scientist Biotechnology CO., Ltd. | SC0001 | |
| glass slide | Nantong Mevid Life Science Co., Ltd. | 220518001 | |
| Gold-conjugated Goat anti-rabbit lgG | Sangon Biotech (Shanghai) Co.,Ltd. | D111094 | |
| Hemostatic forceps (12.5 cm) | Anqisheng Biotechnological Co., Ltd. | PL068 | |
| Hemostatic forceps (14 cm) | Anqisheng Biotechnological Co., Ltd. | PL002 | |
| Isoflurane | Rayward Life Technology Co., Ltd. | 2024071201 | |
| L. R. White Resin | Tianjin Tainuo Science and Technology Co., Ltd. | AGR1281A | |
| Lead citrate | SPI (US) | GA10701 | |
| Needle holder | Jiachi Medical Technology Co., Ltd. | 10044036898028 | |
| Osmium tetroxide | TED PELLA (US) | 4008-220501 | |
| PBS | Servicebio | G4202 | |
| Rabbit polyclonal antibody to cytochrome c | Affinity Biosciences, Ltd. | AF0146 | |
| Rats | Beijing Huafukang Biotechnology Co., Ltd. | 110322241102187881 | |
| SPI-Pon 812 embedding resin kit | SPI(US) | GS02660 | |
| Stereomicroscope | Sunny Optical Technology Co., Ltd. | Soptop SZMN | |
| Straight headed scissors (10 cm) | Anqisheng Biotechnological Co., Ltd. | PL063 | |
| Straight ophthalmic forceps (10cm) | Shanghai Medical Equipment Co., Ltd. | 211001 | |
| Surgical scissors | Rayward Life Technology Co., Ltd. | S14001-10 | |
| Transmission electron microscopy | Hitachi (Japan), Ltd. | HT7800 | |
| ultramicrotome | Leica(Germany) | UC7 | |
| Uranium acetate | SPI (US) | GS02624 |
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