生信论文的套路
- ONCOMINE从全景、亚型两个维度做表达差异分析；
- 临床标本从蛋白水平确认（或HPA数据库），很重要；
- Kaplan-Meier Plotter从临床意义的角度阐明其重要性；
- cBio-portal数据库做基因组学的分析（机制一）；
- STRING互作和GO/KEGG分析探讨可能的信号通路（机制二）；
- TISIDB/TIMER分析肿瘤免疫特征（机制三）。
引文的基本内容：介绍背景（一段或两段）、提出问题（一段），解决问题（一段或2段）。一般引文介绍3~5段。
- 疾病或基因的背景介绍；
- 前人研究的成果、现实情况，存在的问题；
- 阐明研究原因或意义。介绍研究的性质、范畴及其重要性，突出研究目的和待解决的科学问题；
- 研究方法，新发现和意义。
写作举例--生信论文40--三阴性乳腺癌。
第一段，介绍乳腺癌的背景。先介绍乳腺癌的流行病学和目前存在问题，接着对乳腺癌的病理亚型进行详细总结（乳腺癌的写作必定涉及病理分型，这是基本要求），引出免疫治疗和科学问题；最后，用while、even with和therefore引出重要性和紧迫性。
Breast cancer (BRCA) is a prevalent malignancy in female and with the tendency to occur in younger women worldwide.1 Despite the major progress was received in early screening and later treatment strategies for BRCA, the patients who under remission still meet the challenges of tumor relapse or metastasis events.2 Based on the different molecular signatures, such as human epidermal growth factor receptor‐2 (HER2), progesterone receptors (PR) and estrogen receptors (ER), four subtypes of BRCA could be divided, including basal‐like (ER-, PR-, and HER2-), HER2(ER-, PR-, and HER2 ), luminal A (ER and/or PR , and HER2-), and luminal B (ER and/or PR , HER2 ).3 Recently, HER2 targeted (like Trastuzumab) and hormone therapy (such as Everolimus and Anastrozole) have dramatically improved the survival rates of patients with HER2 positive and hormone receptor positive, respectively.4 While triple‐negative breast cancer (TNBC), as the dominant type of basal‐like subtype and unlike other subtypes of BRCA, has no specific therapeutic strategy due to the high heterogeneity and early metastasis. Even with the standard chemotherapy regimens, only 20% of patients with TNBC benefit. Therefore, patients with TNBC always have a predisposition to the worst prognosis.
第三段，进一步阐释乳腺癌与肿瘤浸润的关系。芒果认为，本段开始部分衔接和过渡的不好（绿色背景部分），最好直接切入免疫浸润的主题。后面介绍乳腺癌的免疫逃逸和免疫治疗，思路还是蛮清楚的，值得借鉴。
To reveal the heterogeneity of TNBC, some studies had described the expression profile–based characteristics and successfully divided TNBC into four subtypes from genomic and transcriptomic landscape, including mesenchymal‐like, basal‐like immune‐suppressed, immunomodulatory, and luminal androgen receptor (LAR). Except the LAR, the mechanisms of the other three subtypes were all involved in the immune‐related pathways, suggesting that the high immunogenicity in TNBC initiation.5 Meanwhile, other researchers had classified TNBC expression profiles into three microenvironment clusters with distinct potential immune escape mechanisms using multiomics data.6 These evidence suggested that immune escape mechanisms might be the determinant factor for TNBC heterogeneity. Furthermore, The molecule‐based immunotherapy has been achieved in some malignant cancers, like melanoma or non–small cell lung cancer, by targeting programmed death ligand‐1, programmed death‐1, and cytotoxic T lymphocyte–associated antigen 4 (CTLA4).7,8 Therefore, to elucidate the underlying immune escape mechanisms and screen the actionable targets for immunotherapy might be greatly significant to achieve the precise treatment for TNBC.
第三段介绍BTN3A (CD277)基因的背景，开门见山介绍其功能（最重要），先介绍其在免疫调节中的作用（蓝色），然后引出与肿瘤的关系，引出科学问题。
Butyrophilin subfamily 3 (BTN3A, CD277), as a B7 family member, composes the homolog at the cytomembrane and acts as the immunoglobulins receptors or biomarkers for various immune cells.9Studies had suggested that BTN3A exerts as a crucial role in helping Vγ9Vδ2 T cells recognize tumor cells through T‐cell receptor mediated sensing of phosphoAntigens,10 and agonists (or antagonist) of BTN3A could enhance (or abrogate) Vγ9Vδ2 T cell–mediated lysis of tumor cells.11,12 BTN3A2, as well as BTN3A1 and BTN3A3, belongs to the BTN3A subfamily and is the component of BTN3A. It was suggested that the higher BTN3A2 expression in OV, whether at the messenger RNA (mRNA) or protein level, had an association with T‐cell infiltration and a better prognosis.13 Nevertheless, the underlying role of BTN3A2 in regulating the immune infiltration and prognosis of TNBC are still unclear.
第四段，解决问题，总结式提出BTN3A2与预后、免疫浸润的关系，再用Besides介导免疫浸润及相关分子机制的介绍。层次递进，但芒果不推荐这种方式，头轻脚重，总结部分内容偏少，而免疫浸润和机制的描述过多，给人感觉不协调。个人建议，仅供参考。
In this study, BTN3A2 was identified as a special diagnostic and independently prognostic marker for TNBC and was highly correlated with immune cells infiltration. Besides, BTN3A2 was positively correlated with general T cells, CD8 T cells, Th1 cells, dendritic cells (DCs) infiltrations, and T cells exhaustion in TNBC. T‐cell receptor interaction and nuclear factor‐κB (NF‐κB) signaling pathways might be the involved mechanisms of BTN3A2 regulating the immune infiltration. The study shed light on the relationship of BTN3A2 with diagnose and prognosis of TNBC and uncovered the mechanism of BTN3A2 in TNBC immunology.
与生信论文36、37相比，该论文写作的思路并不值得推荐，供果友们参考。
