生物技术通报 ›› 2023, Vol. 39 ›› Issue (6): 158-170.doi: 10.13560/j.cnki.biotech.bull.1985.2022-1190
收稿日期:
2022-09-26
出版日期:
2023-06-26
发布日期:
2023-07-07
通讯作者:
任晓亮,男,博士,副研究员,研究方向:线虫遗传发育与转录调控;E-mail: xlren@qdio.ac.cn作者简介:
赵金玲,女,硕士研究生,研究方向:线虫遗传发育与转录调控;E-mail: zhaojl21@qdio.ac.cn
基金资助:
ZHAO Jin-ling1,3(), AN Lei1,3, REN Xiao-liang1,2()
Received:
2022-09-26
Published:
2023-06-26
Online:
2023-07-07
摘要:
单细胞转录组测序技术使人们摆脱了细胞异质性问题的干扰,从而在单个细胞水平实现对基因表达及转录调控机制的探索,以及对不同细胞亚群和特殊细胞类型的识别,对系统发育领域的研究具有重要意义。传统模式生物秀丽隐杆线虫(Caenorhabditis elegans)由于体细胞数目固定、细胞分化路径清晰等特点,近年来成为了单细胞转录组学研究的重要模型。本文对目前单细胞转录组测序技术的发展现状进行综述,总结其在秀丽隐杆线虫的细胞谱系分析、单细胞轨迹推断以及神经元细胞图谱等研究工作中的应用情况,并对未来的研究方向作进一步展望。
赵金玲, 安磊, 任晓亮. 单细胞转录组测序技术及其在秀丽隐杆线虫中的应用[J]. 生物技术通报, 2023, 39(6): 158-170.
ZHAO Jin-ling, AN Lei, REN Xiao-liang. Development of Single Cell Transcriptome Sequencing Technology and Its Application in Caenorhabditis elegans[J]. Biotechnology Bulletin, 2023, 39(6): 158-170.
名称 Name | 空间编码方法 Spatial encoding method | 目标 Target | 靶向性 Approach | 研究对象 Subjects of research | 亚细胞水平Subcellular | 参考文献 Reference |
---|---|---|---|---|---|---|
HDST | 条形码珠阵列 | mRNAs | 否 | 小鼠嗅觉细胞 | 是 | [ |
Slide-seq | 条形码珠阵列 | mRNAs | 否 | 小鼠脑 | 否 | [ |
LCM | 显微切割 | mRNAs | 否 | 小鼠脊髓 | 否 | [ |
Geo-seq | 显微切割 | mRNAs | 否 | 小鼠早期胚胎 | 否 | [ |
seqFISH | 单分子荧光原位杂交 | RNA | 是 | 小鼠脑、嗅球 | 是 | [ |
MERFISH | 单分子荧光原位杂交 | RNA | 是 | 人的大脑皮层 | 是 | [ |
FISSEQ | 条形码原位靶向 | mRNAs | 否 | 人原代成纤维细胞 | 是 | [ |
ISS | 条形码原位靶向 | mRNAs | 是 | 人乳腺癌组织 | 是 | [ |
STARmap | 条形码原位靶向 | mRNAs | 是 | 小鼠脑组织切片 | 是 | [ |
SPLiT-seq | 混合分离 | RNA | 是 | 小鼠大脑和脊髓细胞 | 否 | [ |
PETRI-seq | 混合分离 | mRNAs | 是 | 细菌 | 是 | [ |
DBiT-seq | 混合分离 | mRNAs | 是 | 小鼠胚胎 | 否 | [ |
表1 单细胞空间转录组测序技术
Table 1 Single cell spatial transcriptome sequencing technologies
名称 Name | 空间编码方法 Spatial encoding method | 目标 Target | 靶向性 Approach | 研究对象 Subjects of research | 亚细胞水平Subcellular | 参考文献 Reference |
---|---|---|---|---|---|---|
HDST | 条形码珠阵列 | mRNAs | 否 | 小鼠嗅觉细胞 | 是 | [ |
Slide-seq | 条形码珠阵列 | mRNAs | 否 | 小鼠脑 | 否 | [ |
LCM | 显微切割 | mRNAs | 否 | 小鼠脊髓 | 否 | [ |
Geo-seq | 显微切割 | mRNAs | 否 | 小鼠早期胚胎 | 否 | [ |
seqFISH | 单分子荧光原位杂交 | RNA | 是 | 小鼠脑、嗅球 | 是 | [ |
MERFISH | 单分子荧光原位杂交 | RNA | 是 | 人的大脑皮层 | 是 | [ |
FISSEQ | 条形码原位靶向 | mRNAs | 否 | 人原代成纤维细胞 | 是 | [ |
ISS | 条形码原位靶向 | mRNAs | 是 | 人乳腺癌组织 | 是 | [ |
STARmap | 条形码原位靶向 | mRNAs | 是 | 小鼠脑组织切片 | 是 | [ |
SPLiT-seq | 混合分离 | RNA | 是 | 小鼠大脑和脊髓细胞 | 否 | [ |
PETRI-seq | 混合分离 | mRNAs | 是 | 细菌 | 是 | [ |
DBiT-seq | 混合分离 | mRNAs | 是 | 小鼠胚胎 | 否 | [ |
细胞类型 Cell type | 标记基因 Marker genes |
---|---|
肌肉和中胚层 Muscle and mesoderm | ceh-13, ceh-34, cup-4, cwn-1, dmd-4, dsc-1, egl-20, ehn-3, exp-1, eya-1, glb-26, hlh-1, hlh-8, let-381, lgc-26, mig-1, mls-1, myo-3, pal-1, sfrp-1, unc-30, unc-62, unc-39 |
咽 Pharynx | aff-1, agr-1, ceh-2, ceh-6, ceh-19, ceh-22, ceh-45, cwn-2, dmd-4, elt-4, eyg-1, fos-1, glr-8, gly-15, hlh-6, inx-12, inx-20, irx-1, lec-8, let-23, lys-8, mlt-8, mlt-11, nhr-25, nhr-67, nhr-239, pax-1, phat-1, phat-2, phat-5, ref-1, ser-2, slt-1, spp-7, tnc-2, tni-4, tnt-4, ttx-1, unc-62, unc-129, W05B10.4 |
导管和气孔 Duct and pore | aff-1, ceh-37, grl-2, irx-1 |
肠 Intestine | ceh-37, cpr-1, faah-1, irg-7, pal-1, pbo-4, psa-3, ZC204.12 |
皮下组织和侧线细胞 Hypodermis and seam cells | ahr-1, bus-4, bus-8, bus-12, ceh-13, ceh-16, ceh-32, egl-17, elt-1, elt-3, elt-6, lin-12, lin-39, lin-44, mab-5, pax-3, plx-2, rnt-1, slt-1, tbx-2, tbx-8, tbx-9, unc-62, unc-130, vab-3, vab-7 |
胶质细胞和排泄细胞 Glia and excretory cells | aat-1, aff-1, aqp-7, ceh-6, ceh-32, ceh-37, eak-3, eak-6, grd-15, grl-18, grl-12, grl-2, hlh-11, inx-12, inx-13, irx-1, kcc-3, let-23, lim-6, mls-2, mlt-8, mltn-13, nas-31, nhr-25, pros-1, qua-1, sdf-9, ser-2, slt-1, sym-1, unc-62, wrt-6, F52E1.2, F16F9.3, K08D12.4, K09F5.6 |
早期胚胎、生殖腺和直肠 Early embryo,germline and rectum | glh-1, nos-1, pgl-1 |
纤毛神经元 Ciliated neurons | agr-1, bas-1, cat-2, cat-4, capa-1, ceh-13, ceh-19, ceh-36, che-1, cil-7, cng-2, cog-1, cwn-2, dac-1, daf-11, dat-1, deg-1, dhc-3, dyla-1, flp-3, gcy-8, gcy-9, gcy-11, gcy-18, gcy-23, gcy-31, gcy-32, gcy-33, gcy-35, gcy-36, gcy-37, ns-6, klp-6, nhr-6, nhr-67, nhr-216, ocr-1, ocr-4, odr-7, osm-10, pax-2, pcrg-1, pdf-1, sox-2, sptf-1, srb-6, srd-23, srh-74, ssu-1, tba-6, tba-9, tbx-2, trx-1, ttx-1, unc-42, unc-62, xbx-9, C47D2.1, F15A4.5, F09E8.8, K04D7.6, M04B2.6, R102.2 |
非纤毛神经元和纤毛神经元 Non-ciliated neurons and ciliated neurons | ceh-6, che-7, dop-1, flr-4 |
非纤毛神经元 Non-ciliated neurons | acc-1, acc-2, ace-3, acr-15, acr-16, acr-23, acy-2, alr-1, aptf-1, ast-1, bus-18, ceh-6, ceh-10, ceh-17, ceh-24, ceh-27, ceh-31, ceh-32, ceh-34, ceh-43, ceh-63, ceh-75, cex-1, deg-3, des-2, dop-5, eat-4, egl-5, egl-20, fax-1, flp-1, flp-2, flp-4, flp-9, flp-11, flp-12, flp-13, flp-18, flp-22, gbb-1, gbb-2, gcy-35, glb-17, glc-3, glr-1, glr-2, glr-3, glr-4, glr-5, glr-6, glr-8, gpa-2, gpa-14, hlh-13, hlh-14, hlh-34, ins-1, inx-19, irx-1, lad-2, lim-4, lim-6, lin-11, lin-44, lite-1, mab-9, mbr-1, mec-1, mec-3, mec-7, mec-17, mgl-1, mls-2, mod-5, nhr-67, nlp-7, nlp-12, nlp-15, nlp-17, nmr-2, nob-1, odr-2, pdf-1, pks-1, rig-3, rig-4, rig-5, ser-2, ser-4, ser-6, slt-1, snet-1, snf-11, sox-2, sox-3, tbh-1, tbx-2, tdc-1, tmc-1, ttx-3, twk-16, unc-3, unc-4, unc-6, unc-7, unc-17, unc-25, unc-29, unc-30, unc-42, unc-46, unc-47, unc-62, unc-86, unc-130, vab-7, vab-8, vab-15, zig-5, C35B1.7, F26A10.1, F59E11.7, F17C11.2, K07C5.9, Y43F8B.20 |
直肠细胞 Rectal cells | ceh-6, ceh-27, daf-6, dve-1, egl-20, egl-38, elt-3, mab-9, mom-2, nac-2, nhr-25, pal-1, pha-4, ref-2, tat-4 |
表2 末端细胞类型注释的标记基因
Table 2 Marker genes for terminal cell type annotations
细胞类型 Cell type | 标记基因 Marker genes |
---|---|
肌肉和中胚层 Muscle and mesoderm | ceh-13, ceh-34, cup-4, cwn-1, dmd-4, dsc-1, egl-20, ehn-3, exp-1, eya-1, glb-26, hlh-1, hlh-8, let-381, lgc-26, mig-1, mls-1, myo-3, pal-1, sfrp-1, unc-30, unc-62, unc-39 |
咽 Pharynx | aff-1, agr-1, ceh-2, ceh-6, ceh-19, ceh-22, ceh-45, cwn-2, dmd-4, elt-4, eyg-1, fos-1, glr-8, gly-15, hlh-6, inx-12, inx-20, irx-1, lec-8, let-23, lys-8, mlt-8, mlt-11, nhr-25, nhr-67, nhr-239, pax-1, phat-1, phat-2, phat-5, ref-1, ser-2, slt-1, spp-7, tnc-2, tni-4, tnt-4, ttx-1, unc-62, unc-129, W05B10.4 |
导管和气孔 Duct and pore | aff-1, ceh-37, grl-2, irx-1 |
肠 Intestine | ceh-37, cpr-1, faah-1, irg-7, pal-1, pbo-4, psa-3, ZC204.12 |
皮下组织和侧线细胞 Hypodermis and seam cells | ahr-1, bus-4, bus-8, bus-12, ceh-13, ceh-16, ceh-32, egl-17, elt-1, elt-3, elt-6, lin-12, lin-39, lin-44, mab-5, pax-3, plx-2, rnt-1, slt-1, tbx-2, tbx-8, tbx-9, unc-62, unc-130, vab-3, vab-7 |
胶质细胞和排泄细胞 Glia and excretory cells | aat-1, aff-1, aqp-7, ceh-6, ceh-32, ceh-37, eak-3, eak-6, grd-15, grl-18, grl-12, grl-2, hlh-11, inx-12, inx-13, irx-1, kcc-3, let-23, lim-6, mls-2, mlt-8, mltn-13, nas-31, nhr-25, pros-1, qua-1, sdf-9, ser-2, slt-1, sym-1, unc-62, wrt-6, F52E1.2, F16F9.3, K08D12.4, K09F5.6 |
早期胚胎、生殖腺和直肠 Early embryo,germline and rectum | glh-1, nos-1, pgl-1 |
纤毛神经元 Ciliated neurons | agr-1, bas-1, cat-2, cat-4, capa-1, ceh-13, ceh-19, ceh-36, che-1, cil-7, cng-2, cog-1, cwn-2, dac-1, daf-11, dat-1, deg-1, dhc-3, dyla-1, flp-3, gcy-8, gcy-9, gcy-11, gcy-18, gcy-23, gcy-31, gcy-32, gcy-33, gcy-35, gcy-36, gcy-37, ns-6, klp-6, nhr-6, nhr-67, nhr-216, ocr-1, ocr-4, odr-7, osm-10, pax-2, pcrg-1, pdf-1, sox-2, sptf-1, srb-6, srd-23, srh-74, ssu-1, tba-6, tba-9, tbx-2, trx-1, ttx-1, unc-42, unc-62, xbx-9, C47D2.1, F15A4.5, F09E8.8, K04D7.6, M04B2.6, R102.2 |
非纤毛神经元和纤毛神经元 Non-ciliated neurons and ciliated neurons | ceh-6, che-7, dop-1, flr-4 |
非纤毛神经元 Non-ciliated neurons | acc-1, acc-2, ace-3, acr-15, acr-16, acr-23, acy-2, alr-1, aptf-1, ast-1, bus-18, ceh-6, ceh-10, ceh-17, ceh-24, ceh-27, ceh-31, ceh-32, ceh-34, ceh-43, ceh-63, ceh-75, cex-1, deg-3, des-2, dop-5, eat-4, egl-5, egl-20, fax-1, flp-1, flp-2, flp-4, flp-9, flp-11, flp-12, flp-13, flp-18, flp-22, gbb-1, gbb-2, gcy-35, glb-17, glc-3, glr-1, glr-2, glr-3, glr-4, glr-5, glr-6, glr-8, gpa-2, gpa-14, hlh-13, hlh-14, hlh-34, ins-1, inx-19, irx-1, lad-2, lim-4, lim-6, lin-11, lin-44, lite-1, mab-9, mbr-1, mec-1, mec-3, mec-7, mec-17, mgl-1, mls-2, mod-5, nhr-67, nlp-7, nlp-12, nlp-15, nlp-17, nmr-2, nob-1, odr-2, pdf-1, pks-1, rig-3, rig-4, rig-5, ser-2, ser-4, ser-6, slt-1, snet-1, snf-11, sox-2, sox-3, tbh-1, tbx-2, tdc-1, tmc-1, ttx-3, twk-16, unc-3, unc-4, unc-6, unc-7, unc-17, unc-25, unc-29, unc-30, unc-42, unc-46, unc-47, unc-62, unc-86, unc-130, vab-7, vab-8, vab-15, zig-5, C35B1.7, F26A10.1, F59E11.7, F17C11.2, K07C5.9, Y43F8B.20 |
直肠细胞 Rectal cells | ceh-6, ceh-27, daf-6, dve-1, egl-20, egl-38, elt-3, mab-9, mom-2, nac-2, nhr-25, pal-1, pha-4, ref-2, tat-4 |
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