Identification of tumor-specific neoantigens and immune clusters of hepatocellular carcinoma for mRNA vaccine development.

BACKGROUND: To screen efficacious neoantigens for the development of LIHC mRNA vaccines, construct LIHC immune clusters, and therefore select patients who might benefit from vaccination. METHODS: RNA-seq data and clinical information of 371 TCGA-LIHC and 231 ICGC-LIHC cohorts were downloaded. Differentially expressed genes and their associations with prognosis were analyzed by GEPIA, genetic alterations were examined in the cBioPortal portal, and the association between genes and immune infiltrating cells was explored by TIMER. The immune clusters were constructed by consistency clustering, and the immune landscape was described using CIBERSORT. RESULTS: POLR3C and KPNA2 were identified as LIHC tumor neoantigens related to inferior prognosis and antigen-presenting cell infiltration. In addition, three immune clusters (IC1, IC2 and IC3) with significant differences in molecular, immune cytological, and clinical features were identified in both the TCGA and ICGC LIHC cohorts. Immune "hot" phenotype IC3 displayed a better survival than IC2, and immune "cold" phenotype IC1 exhibited a high tumor mutation burden. CONCLUSION: In conclusion, for the development of anti-LIHC mRNA vaccines, we identified efficacious neoantigens POLR3C and KPNA2, profiled the tumor microenvironment of LIHC, and identified IC1 patients as the subgroup who might not most benefit from vaccination.

TBC1D3 promotes neural progenitor proliferation by suppressing the histone methyltransferase G9a.

Genomic changes during human linage evolution contribute to the expansion of the cerebral cortex to allow more advanced thought processes. The hominoid-specific gene TBC1D3 displays robust capacity of promoting the generation and proliferation of neural progenitors (NPs), which are thought to contribute to cortical expansion. However, the underlying mechanisms remain unclear. Here, we found that TBC1D3 interacts with G9a, a euchromatic histone lysine N-methyltransferase, which mediates dimethylation of histone 3 in lysine 9 (H3K9me2), a suppressive mark for gene expression. TBC1D3 displayed an inhibitory role in G9a's histone methyltransferase activity. Treatment with G9a inhibitor markedly increased NP proliferation and promoted human cerebral organoid expansion, mimicking the effects caused by TBC1D3 up-regulation. By contrast, blockade of TBC1D3/G9a interaction to disinhibit G9a caused up-regulation of H3K9me2, suppressed NP proliferation, and impaired organoid development. Together, this study has demonstrated a mechanism underlying the role of a hominoid-specific gene in promoting cortical expansion.

[Molecular and cellular mechanisms of cortical expansion and folding in brain development and evolution].

During the evolution from primates to humans, the size of cerebral cortex is increased by forming more gyri and sulci, which is believed to be highly associated with cognitive abilities and the basis of higher brain functions in humans. Accumulating lines of evidence have shown that the cortical size is regulated both by protein-coding genes and non-coding RNAs. In particular, the recently identified outer radial glial cells (oRGs) distributed in the outer subventricular zone (oSVZ) of gyrencephalic brains, have been considered to be important for cortical expansion and folding. This review summarizes recent progresses in the understanding of cortex expansion and discusses the potential molecular and cellular mechanisms of cortical folding.

The hominoid-specific gene TBC1D3 promotes generation of basal neural progenitors and induces cortical folding in mice.

Cortical expansion and folding are often linked to the evolution of higher intelligence, but molecular and cellular mechanisms underlying cortical folding remain poorly understood. The hominoid-specific gene TBC1D3 undergoes segmental duplications during hominoid evolution, but its role in brain development has not been explored. Here, we found that expression of TBC1D3 in ventricular cortical progenitors of mice via in utero electroporation caused delamination of ventricular radial glia cells (vRGs) and promoted generation of self-renewing basal progenitors with typical morphology of outer radial glia (oRG), which are most abundant in primates. Furthermore, down-regulation of TBC1D3 in cultured human brain slices decreased generation of oRGs. Interestingly, localized oRG proliferation resulting from either in utero electroporation or transgenic expression of TBC1D3, was often found to underlie cortical regions exhibiting folding. Thus, we have identified a hominoid gene that is required for oRG generation in regulating the cortical expansion and folding.

Semaphorin 3A activates the guanosine triphosphatase Rab5 to promote growth cone collapse and organize callosal axon projections.

Axon guidance (pathfinding) wires the brain during development and is regulated by various attractive and repulsive cues. Semaphorin 3A (Sema3A) is a repulsive cue, inducing the collapse of axon growth cones. In the mammalian forebrain, the corpus callosum is the major commissure that transmits information flow between the two hemispheres, and contralateral axons assemble into well-defined tracts. We found that the patterning of callosal axon projections in rodent layer II and III (L2/3) cortical neurons in response to Sema3A was mediated by the activation of Rab5, a small guanosine triphosphatase (GTPase) that mediates endocytosis, through the membrane fusion protein Rabaptin-5 and the Rab5 guanine nucleotide exchange factor (GEF) Rabex-5. Rabaptin-5 bound directly to Plexin-A1 in the Sema3A receptor complex [an obligate heterodimer formed by Plexin-A1 and neuropilin 1 (NP1)]; Sema3A enhanced this interaction in cultured neurons. Rabaptin-5 bridged the interaction between Rab5 and Plexin-A1. Sema3A stimulated endocytosis from the cell surface of callosal axon growth cones. In utero electroporation to reduce Rab5 or Rabaptin-5 impaired axon fasciculation or caused mistargeting of L2/3 callosal projections in rats. Overexpression of Rabaptin-5 or Rab5 rescued the defective callosal axon fasciculation or mistargeting of callosal axons caused by the loss of Sema3A-Plexin-A1 signaling in rats expressing dominant-negative Plexin-A1 or in NP1-deficient mice. Thus, our findings suggest that Rab5, its effector Rabaptin-5, and its regulator Rabex-5 mediate Sema3A-induced axon guidance during brain development.

[Macroscopical anatomic structure of acupoint "Shangyang" (LI 1), "Erjian" (LI 2), "Sanjian" (LI 3), "Hegu" (LI 4), and "Quchi" (LI 11) regions in the forelimb in rabbits].

OBJECTIVE: To observe the structure of acupoints: "Shangyang" (LI 1), "Erjian" (LI 2), "Sanjian" (LI 3), "Hegu" (LI 4) and "Ouchi" (LI 11) of the Yangming Meridian in the rabbit's forelimb. METHODS: The acupoints were first located in accordance with the related atlas of rabbits and confirmed by low resistance and higher electric potential determinations by using a "multipurpose electronic acupoint detection and therapeutic instrument". Then the animals under anesthesia were killed by intravenous injection of air embolism, perfused with 5% natrium citricum first, acetic ether containing acrylonitrile-butadiene-styrene copolymer, and 5% dicapryl phthalate, blue and red pigments for paintings via subclavian artery, respectively. After routinely inserting an acupuncture needle into the acupoint, the local tissues (muscles, blood vessels and nerves) of the acupoints mentioned above were dissected layer by layer and their relations with the needle were observed under microscope. RESULTS: "Erjian" (LI 2) is situated at the depression site distal to the second metacarpophalangeal joint on the radial side. "Sanjian" (LI 3) is located at the depression site proximal to the second metacarpophalangeal joint on the radial side. The shallow-layers of "Shangyang" (LI 1), "Erjian" (LI 2), "Sanjian" (LI 3), "Hegu" (LI 4) and "Quchi" (LI 11) mainly contain cephalic vein and shallow branches of the radial nerve, and their deep layers chiefly contain radial artery and its branches, and the median nerve. CONCLUSION: "Shangyang" (LI 1), "Erjian" (LI 2), "Sanjian" (LI 3), "Hegu" (LI 4) and "Quchi" (LI 11) have a close association with the cephalic vein,radial artery,radial vein and its branches,superficial branch of radial nerve and the median nerve,which constitutes the morphological basis of the five points.