Laser Capture Microdissection Research Articles

Accurate diagnosis of early-stage lung cancer by targeting lipid droplets with a two-photon near-infrared fluorescence probe

Clinically, solid nodules with adenocarcinoma (SN–ADC) exhibit faster growth and greater invasiveness than ground-glass nodules with adenocarcinoma (GGN-ADC). Metabolic reprogramming is a critical feature of tumor cells and may facilitate the rapid progression of early-stage lung cancer. Herein, we used laser microdissection to precisely isolate malignant regions from five SN–ADC and six GGN–ADC samples for proteomic analysis. Bioinformatic analysis, western blotting, and electron microscopy conducted in this study revealed a significant upregulation of lipid droplet-associated protein (PLIN2) and marked increase in lipid droplet (LD) accumulation in SN–ADC tissues. Consequently, a novel two-photon near-infrared fluorescence probe was developed to monitor the dynamic changes in LDs in lung cancer cells. Further, experimental validation confirmed the effectiveness of the LD probe (LD-probe) in monitoring the changes in LDs in tumor cells and distinguishing LD differences between tumor and normal tissues. In particular, the probe successfully detected significant differences in LD behavior between SN–ADC and GGN–ADC in early-stage lung cancer. Thus, this study developed a rapid and effective tool for the diagnosis of early-stage lung cancer. The proposed method offers deeper insight into the monitoring of the behavior of LDs in tumor cells, with potential clinical applications.

Temporal and spatial layout of endocannabinoid system components in the mouse suprachiasmatic nucleus

Environmental light serves as the main entraining signal for the central circadian pacemaker, the suprachiasmatic nucleus of the hypothalamus (SCN). To shift clock timing with the changing environment, minute adjustments are necessary and the endocannabinoid system (ECS) acts as a neuromodulatory signaling mechanism in the SCN. These systems exert bidirectional effects on one another, still, limited knowledge exists about the role of endocannabinoids in circadian rhythm regulation. Therefore, we investigated the temporal and spatial molecular layouts of the ECS in the SCN of male and female C57BL/6J mice. We utilized laser capture microdissection and quantitative RT-PCR to investigate the ECS temporal layout in the SCN, detected 13 of 19 examined ECS components, and followed up with two 24-hour time course experiments, one under 12:12 light/dark and one under constant dark conditions. All enzymatic machinery related to endocannabinoid synthesis and degradation investigated were found present; however, only cannabinoid receptor 1 (Cnr1) was detected from the 6 ECS related receptors investigated. Cosinor analysis revealed circadian rhythms in many components in both sexes and lighting conditions. Next, we investigated the spatial localization of ECS components in the SCN with RNAscope in situ hybridization. Some genes, such as Cnr1, were more highly expressed in neurons with others, such as Fabp7, were elevated in astrocytes. Cnr1 levels were highest in neurons that do not express the neuropeptides Avp or Vip, and lowest in Vip neurons. Our results support the idea that locally regulated ECS signaling through neuronal CB1 modulates circadian clock function.

Laser Capture Microdissection of Tertiary Lymphoid Structures from Formalin-Fixed Paraffin-Embedded Sections of Canine Cutaneous and Subcutaneous Sarcomas for NanoString Direct RNA Counting.

Laser capture microdissection (LCM) of formalin-fixed, paraffin-embedded sections is a way to analyze gene expression of morphologically distinct areas of tissue, as microscopically visualized with stained tissue sections. Herein, I describe a method for laser dissecting lymphoid aggregates in canine cutaneous and subcutaneous sarcomas and their adjacent sarcoma tissue to determine the differential expression of RNA as determined by NanoString® nCounter technology. Canine soft tissue sarcomas (STS) are diversely derived mesenchymal neoplasms that, regardless of exact histogenesis, behave similarly and thus have been grouped together as a diagnostic entity. The risk of recurrence and/or metastasis depends on the extent of surgical excision and histologic grade. Lymphoid aggregates are described in these tumors but have not been characterized. In humans, lymphoid aggregates characterized as tertiary lymphoid structures (TLS) improve the prognosis of several tumors, including sarcomas. We sought to determine if RNA expressed by lymphoid aggregates in canine sarcomas was compatible with TLS RNA expression. This chapter describes tissue preparation, staining, laser capture microdissection, and RNA isolation in preparation for digital RNA counting.

Methods for Selective Gene Expression Profiling in Single Tertiary Lymphoid Structure Using Laser Capture Microdissection.

Tertiary lymphoid structures (TLS) are de novo lymphoid formations that are induced within tissues during inflammatory episodes. TLS have been reported at various anatomic sites and in many different contexts like cancer, infections, autoimmunity, graft rejection, and idiopathic diseases. These inducible, ectopic, and transient lymphoid structures exhibit the prototypical architecture found within secondary lymphoid organs (SLO) and have been increasingly recognized as a major driver of local adaptive immune reaction. As TLS emerge within tissues, the isolation in situ and the molecular characterization of these structures are challenging to perform. Laser capture microdissection (LCM) is a powerful tool to isolate selective structural components and cells from frozen or paraffin-embedded tissues. We and other groups previously applied LCM to decipher the molecular network within TLS and uncover their intrinsic connection with the local microenvironment. In this chapter, we describe a detailed LCM method for selecting and isolating TLS in situ to perform comprehensive downstream molecular analyses.

Abstract 4137902: Layer-specific Gene Expression Associated with Intima Hyperplasia in Arterio-venous Fistula

Background: The mechanism of hemodialysis arteriovenous fistula (AVF) vein intima hyperplasia (IH) may be specific to its layers (intima, media, and adventitia) but is poorly understood. To address this gap, we studied layer-specific transcriptomics related to IH in veins of two-stage AVF creation. Methods: Vein samples were collected during the initial creation of brachial artery-basilic vein AVF (1st stage) and vein transposition surgery 6 weeks later (2nd stage) and were sectioned in OCT. Tissues from each layer were separately collected by laser microdissection. Following Takara’s SMARTer Stranded Total RNA-Seq Pico Input protocol, libraries were constructed and sequenced in NovaSeq. The sequencing reads were processed by fastp, aligned to genome GENCODE 45 by STAR and gene-level counts were estimated by RSEM. Intima was assessed by histology. Layer-specific differentially expressed genes in pre-access or AVF veins associated with IH in AVF veins were detected by edgeR and further identified the enriched pathways and predicted functions using Qiagen IPA. Results: 44 veins were collected from 22 patients. 13,522 protein-coding genes that had a raw count of at least 10 in more than 70% of samples were included in analysis. 10 AVF veins had severe IH. Among the layers of pre-access vein, intima had the largest number of genes significantly associated with severe AVF IH and most or all these genes were upregulated (35/4, 26/2, 5/0 for the number of up/downregulated genes in intima, media, and adventitia of pre-access vein, respectively); cellular movement and immune cell trafficking were more strongly activated in intima of pre-access vein with severe AVF IH. No genes in any layer of AVF vein were significantly associated with severe AVF IH. From 1 st to 2 nd stage, more genes significantly changed expression in intima with severe AVF IH than intima without severe AVF IH (197/150 vs 144/93 for up/downregulated genes), while media (20/4 vs 149/31) and adventitia (99/27 vs 196/70) were the opposite; TGFB1, angiotensinogen, and TNF were more strongly activated in intima, while cell survival and migration were diminished in media and adventitia with severe AVF IH, respectively. Conclusion: Intima of pre-access vein has more genes associated with severe AVF IH. The layer-specific gene expression changes during AVF development and predicted functions are associated with AVF IH. These data can be used to develop layer-specific therapies to reduce AVF IH.

RNA Extraction from Rice Immature Embryo Using Laser Capture Microdissection.

Laser capture microdissection (LCM) enables the selective isolation of organs, tissues, and cells from surrounding tissues. Total RNA extracted from small tissue sections can be used for a variety of subsequent analysis such as RNA-seq analysis. Here, we describe a method for isolating embryos from rice ovary sections using LCM and extracting total RNA. We successfully obtained sufficient amount of total RNA from a single rice embryo at the globular embryo stage for RNA-seq analysis.

Reevaluating hybrid neurofibroma/schwannoma: Predominance of schwannoma features despite CD34 positivity and initial neurofibroma diagnosis.

Schwannomas consist of both high-cellularity regions (Antoni A area) and hypocellular regions (Antoni B area) in histopathological findings. Neurofibromas characteristically consist of CD34 positive spindle cells with thin, wavy, nuclei and wavy collagen bands. Previous reports have described segments of schwannomas with neurofibroma features as hybrid tumors, although hybrid tumors were diagnosed based on partial CD34 positivity in many previous reports. On the other hand, the Antoni B area of some schwannomas was reported to be positive for CD34. Therefore, the definition of a hybrid tumor has not been clear. The objective of this study was to determine whether only CD34 positive findings in schwannomas could be used to define a hybrid tumor. In the analysis of our patient with schwannomatosis caused by a novel LZTR1 germline mutation, part of the tumor had CD34 positive hypocellular regions. These regions contained no thin, wavy, nuclei, indicating an Antoni B area. Laser microdissection was used to investigate the genetic background and differences in molecular mechanisms between CD34 positive and CD34 negative regions. All mutations identified in CD34 positive regions were also found in CD34 negative regions. Our data could not clear the genetic background of Antoni B which was CD34 positive area. We then reviewed the pathologies of 66 sporadic schwannomas. Histopathological examinations of all schwannomas revealed the absence of thin, wavy, nuclei and wavy collagen bands, and no hybrid tumors were found in any of the cases. Ten of 66 patients were randomly selected for CD34 immunostaining and positivity was found in all cases. Our data suggest that it is difficult to distinguish schwannomas by staining for CD34 alone, as Antoni B areas can also be positive for CD34. Therefore, CD34 staining alone should not be used to diagnose hybrid tumors in patients with schwannomas.

Spatial proteomics of single cells and organelles on tissue slides using filter-aided expansion proteomics.

Hydrogel-based tissue expansion combined with mass spectrometry (MS) offers an emerging spatial proteomics approach. Here, we present a filter-aided expansion proteomics (FAXP) strategy for spatial proteomics analysis of archived formalin-fixed paraffin-embedded (FFPE) specimens. Compared to our previous ProteomEx method, FAXP employed a customized tip device to enhance both the stability and throughput of sample preparation, thus guaranteeing the reproducibility and robustness of the workflow. FAXP achieved a 14.5-fold increase in volumetric resolution. It generated over 8 times higher peptide yield and a 255% rise in protein identifications while reducing sample preparation time by 50%. We also demonstrated the applicability of FAXP using human colorectal FFPE tissue samples. Furthermore, for the first time, we achieved bona fide single-subcellular proteomics under image guidance by integrating FAXP with laser capture microdissection.

Tissue-specific chemical expression and quantitative analysis of bioactive components of Moutan Cortex by laser-microdissection combined with UPLC-Q-Orbitrap-MS technique

Moutan Cortex, is the root bark of Paeonia suffruticosa Andrews, which is classified into three specifications according to whether or not it is peeled and cored: Liandanpi, Guadanpi and whole root. In this study, the cork layer, cortex, phloem and xylem of P. suffruticosa fresh root were precisely separated by laser microdissection technique. UPLC-Q-Orbitrap-MS and UPLC-QQQ-MS techniques were used to analyse the differences in the chemical composition of different tissue parts of P. suffruticosa fresh root and Liandanpi, and to determine the optimal processing method of P. suffruticosa root. As a result, a total of 90 compounds were characterised, among which the cork layer had more types and higher contents of chemical constituents, and the xylem had fewer types and lower contents of chemical constituents. The proportion of xylem is larger, while the type and content of active ingredients is smaller. Therefore, the processing method of removing the wood core and retaining the cork bark can be used in the processing of Moutan Cortex. In this study, laser microdissection and ultra performance liquid chromatography-mass spectrometry were used to provide a theoretical basis for optimising the processing method of Moutan Cortex to enhance its pharmacological effects.

Spatial proteomics of Onchocerca volvulus with pleomorphic neoplasms shows local and systemic dysregulation of protein expression.

Onchocerca volvulus is the agent of onchocerciasis (river blindness) and targeted by WHO for elimination though mass drug administration with ivermectin. A small percentage of adult worms develop pleomorphic neoplasms (PN) that are positively associated with the frequency of ivermectin treatment. Worms with PN have a lower life expectancy and a better understanding about the proteins expressed in PN, and how PN affect protein expression in different tissues could help to elucidate the mechanisms of macrofilaricidal activity of ivermectin. Within a clinical trial of drug combinations that included ivermectin, we detected 24 (5.6%) O. volvulus females with PN by histology of paraffin embedded nodules. To assess the protein inventory of the neoplasms and to identify proteins that may be associated with tumor development, we used laser capture microdissection and highly sensitive mass spectrometry analysis. Neoplasm tissue from three female worms was analyzed, and compared to normal tissues from the body wall, uterus and intestine from the same worms, and to tissues from three females without PN. The healthy females showed all intact embryogenesis. In PN worms, 151 proteins were detected in the body wall, 215 proteins in the intestine, 47 proteins in the uterus and 1,577 proteins in the neoplasms. Only the uterus of one PN female with some stretched intrauterine microfilariae had an elevated number of proteins (601) detectable, while in the uteri of the healthy females 1,710 proteins were detected. Even in tissues that were not directly affected by PN (intestine, body wall), fewer proteins were detected compared to the corresponding tissue of the healthy controls. Immunolocalization of the calcium binding protein OvDig-1 (OVOC8391) confirmed the detection in PN by mass spectrometry. In conclusion we identified proteins that are potentially linked to the development of PN, and systemic dysregulation of protein expression may contribute to worm mortality.

Stromal Expression Profiling Reveals Immune-Driven Adaption to Malignancy in Canine Melanoma Subtypes.

Canine mucosal melanoma (CMM) is the most common oral malignancy in dogs and is significantly more aggressive than its cutaneous counterpart (CCM), yet the reasons for this disparity remain unclear. Cancer-associated stroma (CAS) plays a crucial role in tumour progression, but a detailed understanding of CAS in canine melanoma is missing. To assess stromal reprogramming, we analysed CAS from 21 CMM, 14 CCM and normal stroma from 10 skin and 9 oral mucosa samples by laser-capture microdissection followed by RNA sequencing. Results were assessed in relation to subtypes, prognostic factors including mitotic count (MC), ulceration, necrosis, pigmentation and immune cell infiltration (CD3, CD20 and CD68), scored using immunohistochemistry and RNA in situ hybridisation. Stromal reprogramming was evident in both subtypes but significantly more pronounced in CMM. Immune-excluded tumours exhibited higher MC than desert/cold ones. MC strongly correlated with genes associated with B-cells, T-helper cells and CTLA4 in CCM, suggesting CAS reprogramming to depend on tumour malignancy. Finally, we identify an immune-suppressive stromal signature in a subset of CMM characterised by the downregulation of key immune checkpoints and pathways. Together, these findings provide a solid foundation for understanding the role of CAS in canine melanoma, specific to cutaneous and mucosal subtypes.

HEV ORF2 protein-antibody complex deposits are associated with glomerulonephritis in hepatitis E with reduced immune status

Hepatitis E virus (HEV) infection, one of the most common forms of hepatitis worldwide, is often associated with extrahepatic, particularly renal, manifestations. However, the underlying mechanisms are incompletely understood. Here, we report the development of a de novo immune complex-mediated glomerulonephritis (GN) in a kidney transplant recipient with chronic hepatitis E. Applying immunostaining, electron microscopy, and mass spectrometry after laser-capture microdissection, we show that GN develops in parallel with increasing glomerular deposition of a non-infectious, genome-free and non-glycosylated HEV open reading frame 2 (ORF2) capsid protein. No productive HEV infection of kidney cells is detected. Patients with acute hepatitis E display similar but less pronounced deposits. Our results establish a link between the production of HEV ORF2 protein and the development of hepatitis E-associated GN in the immunocompromised state. The formation of glomerular IgG-HEV ORF2 immune complexes discovered here provides a potential mechanistic explanation of how the hepatotropic HEV can cause variable renal manifestations. These findings directly provide a tool for etiology-based diagnosis of hepatitis E-associated GN as a distinct entity and suggest therapeutic implications.

Tracking the emergence of a novel genotype of Decapod hepanhamaparvovirus in shrimp using laser microdissection and next generation sequencing.

The prevalence of hepatopancreatic diseases in cultured shrimp has increased in recent years. Decapod Hepanhamaparvovirus 1 (DHPV) infection was identified by histology in samples that could not be detected by PCR-based assay for this virus. Employing Laser Microdissection (LMD), we dissected cells containing intranuclear inclusion bodies pathognomonic for DHPV infection from histological sections. Whole Genome Amplification and NGS were used to generate five complete genomes of the novel DHPV isolate that showed identities ranging from 77% to 98% to previously reported isolates. Phylogenetic analyses revealed the DHPV isolate represents a novel genotype, Genotype V. We developed PCR and in situ hybridization methods tailored for the specific detection of this genotype. Our approach of combining LMD with NGS opens avenues for rapid identification of emerging viral pathogens and retrospective studies to understand origin and evolution of viruses showcasing the transformative potential of the innovative approach used in this study.

DAMPs Drive Fibroinflammatory Changes in the Glaucomatous ONH.

The optic nerve head (ONH) is well known to be the initial site of glaucomatous damage; however, the molecular mechanisms initiating this pathology are not fully understood. To further understand the initiating factors in glaucomatous damage we utilized a novel mouse model of glaucoma, B6.EDA+/+ mice, which constitutively express fibronectin containing the extra domain A (FN+EDA). FN+EDA is a known damage-associated molecular pattern (DAMP) that activates Toll-like receptor 4 and elicits a fibro-inflammatory response. Eyes from B6.EDA+/+ and C57BL/6J mice were evaluated for retinal ganglion cell (RGC) death, retinal nerve fiber layer (RNFL) thickness, and optic nerve (ON) damage at 12 months and 22 months of age. ONH sections were isolated using laser capture microdissection for subsequent RNA-sequencing and Gene Set Enrichment Analysis (GSEA). GSEA results were confirmed using immunohistochemical (IHC) staining. B6.EDA+/+ mice exhibit significantly higher intraocular pressure, loss of RGCs, thinning of the RNFL, and progressive levels of ON damage at 12 months and 22 months of age compared to C57BL/6J controls. Protein expression of DAMPs FN+EDA and biglycan was significantly increased in B6.EDA+/+ mice compared to C57BL/6J controls. GSEA analysis identified significantly up- and downregulated gene groupings at both 12 months and 22 months of age, and IHC staining at 12 and 18 months of age demonstrated significant increases of IFNα, IFNβ, and pSTAT1 expression in B6.EDA+/+ mice compared to C57BL/6J controls. Our study characterizes glaucomatous changes to the retina, ON, and ONH over the course of 2 years and identifies novel molecular pathways associated with these pathophysiological changes. These data illustrate the effects of FN+EDA on the fibro-inflammatory response in the aging ONH in a novel mouse model of glaucoma.

Adenosine Metabolism Pathway Alterations in Frontal Cortical Neurons in Schizophrenia.

Schizophrenia is a neuropsychiatric illness characterized by altered neurotransmission, in which adenosine, a modulator of glutamate and dopamine, plays a critical role that is relatively unexplored in the human brain. In the present study, postmortem human brain tissue from the anterior cingulate cortex (ACC) of individuals with schizophrenia (n = 20) and sex- and age-matched control subjects without psychiatric illness (n = 20) was obtained from the Bronx-Mount Sinai NIH Brain and Tissue Repository. Enriched populations of ACC pyramidal neurons were isolated using laser microdissection (LMD). The mRNA expression levels of six key adenosine pathway components-adenosine kinase (ADK), equilibrative nucleoside transporters 1 and 2 (ENT1 and ENT2), ectonucleoside triphosphate diphosphohydrolases 1 and 3 (ENTPD1 and ENTPD3), and ecto-5'-nucleotidase (NT5E)-were quantified using real-time PCR (qPCR) in neurons from these individuals. No significant mRNA expression differences were observed between the schizophrenia and control groups (p > 0.05). However, a significant sex difference was found in ADK mRNA expression, with higher levels in male compared with female subjects (Mann-Whitney U = 86; p < 0.05), a finding significantly driven by disease (t(17) = 3.289; p < 0.05). Correlation analyses also demonstrated significant associations (n = 12) between the expression of several adenosine pathway components (p < 0.05). In our dementia severity analysis, ENTPD1 mRNA expression was significantly higher in males in the "mild" clinical dementia rating (CDR) bin compared with males in the "none" CDR bin (F(2, 13) = 5.212; p < 0.05). Lastly, antipsychotic analysis revealed no significant impact on the expression of adenosine pathway components between medicated and non-medicated schizophrenia subjects (p > 0.05). The observed sex-specific variations and inter-component correlations highlight the value of investigating sex differences in disease and contribute to the molecular basis of schizophrenia's pathology.

A Deficiency in Glutamine-Fructose-6-Phosphate Transaminase 1 (Gfpt1) in Skeletal Muscle Results in Reduced Glycosylation of the Delta Subunit of the Nicotinic Acetylcholine Receptor (AChRδ).

The neuromuscular junction (NMJ) is the site where the motor neuron innervates skeletal muscle, enabling muscular contraction. Congenital myasthenic syndromes (CMS) arise when mutations in any of the approximately 35 known causative genes cause impaired neuromuscular transmission at the NMJ, resulting in fatigable muscle weakness. A subset of five of these CMS-causative genes are associated with protein glycosylation. Glutamine-fructose-6-phosphate transaminase 1 (Gfpt1) is the rate-limiting enzyme within the hexosamine biosynthetic pathway (HBP), a metabolic pathway that produces the precursors for glycosylation. We hypothesized that deficiency in Gfpt1 expression results in aberrant or reduced glycosylation, impairing the proper assembly and stability of key NMJ-associated proteins. Using both in vitro and in vivo Gfpt1-deficient models, we determined that the acetylcholine receptor delta subunit (AChRδ) has reduced expression and is hypo-glycosylated. Using laser capture microdissection, NMJs were harvested from Gfpt1 knockout mouse muscle. A lower-molecular-weight species of AChRδ was identified at the NMJ that was not detected in controls. Furthermore, Gfpt1-deficient muscle lysates showed impairment in protein O-GlcNAcylation and sialylation, suggesting that multiple glycan chains are impacted. Other key NMJ-associated proteins, in addition to AChRδ, may also be differentially glycosylated in Gfpt1-deficient muscle.

Human Tubulointerstitial Responses to Proteinuria Analysed by Proteomics and Laser Capture Microdissection

Human Tubulointerstitial Responses to Proteinuria Analysed by Proteomics and Laser Capture Microdissection

Salinity-Induced Photorespiration in Populus Vascular Tissues Facilitate Nitrogen Reallocation.

Adaptation to abiotic stress is critical for the survival of perennial tree species. Salinity affects plant growth and productivity by interfering with major biosynthetic processes. Detrimental effects of salinity may vary between different plant tissues and cell types. However, spatial molecular mechanisms controlling plant responses to salinity stress are not yet thoroughly understood in perennial trees. We used laser capture microdissection in clones of Populus tremula x alba to isolate palisade and vascular cells of intermediary leaf from plants exposed to 150 mM NaCl for 10 days, followed by a recovery period. Cell-specific changes in proteins and metabolites were determined. Salinity induced a vascular-specific accumulation of proteins associated with photorespiration, and the accumulation of serine, 3-phosphoglycerate and NH4 + suggesting changes in N metabolism. Accumulation of the GLUTAMINE SYNTHETASE 2 protein, and increased GS1.1 gene expression, indicated that NH4 + produced in photorespiration was assimilated to glutamine, the main amino acid translocated in Populus trees. Further analysis of total soluble proteins in stems and roots showed the accumulation of bark storage proteins induced by the salinity treatments. Collectively, our results suggest that the salt-induced photorespiration in vascular cells mediates N-reallocation in Populus, an essential process for the adaptation of trees to adverse conditions.

Phospholipase A2 Receptor (PLA2R)-Positive Membranous Nephropathy by Laser Microdissection and Mass Spectrometry in Patients with Negative Routine Immunofluorescence Microscopy for PLA2R on Kidney Biopsy

Phospholipase A2 Receptor (PLA2R)-Positive Membranous Nephropathy by Laser Microdissection and Mass Spectrometry in Patients with Negative Routine Immunofluorescence Microscopy for PLA2R on Kidney Biopsy

Laser Microdissection and Mass Spectrometry: A Reliable Clinical Test for Detection of Membranous Nephropathy (MN) Antigens

Laser Microdissection and Mass Spectrometry: A Reliable Clinical Test for Detection of Membranous Nephropathy (MN) Antigens