the characteristics of hpv integration in cervical …1 1 the characteristics of hpv integration in...

1

The characteristics of HPV integration in cervical intraepithelial cells 1

2

Weiping Li1，Shuang Tian1，Pengpeng Wang2，Yikun Zang2，Xin Chen3, Yuanqing Yao1*，Weiyang 3

Li4* 4

5 1Department of Obstetrics and Gynecology, Chinese PLA General Hospital, Beijing, P. R. China 6 2MyGenostics Inc., Beijing, P. R. China 7 3 ME Genomics Inc., Shenzhen, P. R. China 8 4Collaborative Innovation Center for Birth Defect Research and Transformation of Shandong 9

Province, Jining Medical University, Jining, Shandong 272067, China 10

11

*Corresponding authors: 12

Yuanqing Yao, Department of Obstetrics and Gynecology, Chinese PLA General Hospital, Beijing, 13

P. R. China, E-mail: [email protected], 14

Weiyang Li, Collaborative Innovation Center for Birth Defect Research and Transformation of 15

Shandong Province, Jining Medical University, Jining, Shandong 272067, China. E-mail: 16

[email protected] 17

18

ABSTRACT: 19

Cervical cancer is one of the most common malignant tumors in gynecology. 20

Deploying HIVID, a cost-effective technique to detect HPV integration sites, our team 21

had studied the characteristics of HPV integrations in cervical exfoliated cells. Our 22

results indicated that both the sample proportion and the number of HPV integrations 23

gradually increased following the development of cervical lesion. Meanwhile, our data 24

also revealed that there were recurrent genes integrated by HPV in cervical exfoliated 25

cells. Collectively, the HPV integration breakpoints were highly enriched in the exon 26

and promoter regions. Intriguingly, the gene pathway analysis indicated that the HPV-27

integrated genes were strongly inclined to pathways of metabolism of xenobiotics by 28

cytochrome P450, chemical carcinogenesis and steroid hormone biosynthesis. In 29

conclusion, this study unveiled the HPV integration patterns and the associated 30

recurrent genes in cervical epithelial exfoliated cells. Altogether, our data suggested 31

that the HPV integrations in cervical exfoliated cells might have vital clinical 32

significance, and probably also diagnostic and/or prognostic values in future clinical 33

applications. 34

35

Key words: HPV integration; Cervical exfoliated cells; Cervical cancer; Characteristics 36

37

mailto:[email protected]

mailto:[email protected]

2

1 Introduction 38

Cervical cancer is one of the most common malignant tumors in gynecology, with an 39

occurring incidence only second to that of breast cancer among all female malignant 40

tumors. In recent years, due to the development of cervical exfoliative cytology, the rate 41

of cervical cancer had been decreased by 70%-80%, as well as the corresponding 42

mortality[1]. It is believed that the sensitivity and specificity of cervical cancer and 43

precancerous lesion diagnosis by cytology were around 47%-62% and 60%-90%, 44

respectively[2]. Suggesting further improvement of the current diagnostic mean is 45

urgently demanded to help identify the high-risk group. 46

More recently, HPV screening had been shown better at predicting cervical cancer 47

than cytology as confirmed by an increasing number of studies. It is acknowledged that 48

HPV infection could be cleared by the host immune system in most of women. 49

Nevertheless, HPV infection in approximately 1-2% of the affected might persist and 50

eventually leading to cervical intraepithelial neoplasia or cervical cancer [3]. The high-51

risk HPV had a clear association with the development of carcinogenesis. During the 52

persist infection of the high-risk HPV, HPV integration events could often be detected, 53

which were well known to cause genome instability, abnormal gene expression in 54

cells[4-6]. In addition, the viral E2 region is often being abrogated upon the HPV 55

integration, resulting in uncontrolled viral replication [7]. An elevating number of 56

research data had now suggested that the DNA integration of high-risk HPV might be 57

pre-requisite and/or driven force of HPV-induced carcinogenesis, the maintenance of 58

malignant phenotype, and the development of cervical cancer[8]. As followed by the 59

ongoing research, the association of HPV integration have been established with the 60

CIN level of the cervix, which could potentially being used as a marker for the cervical 61

cancer risk assessment for those who suffered HPV infection [9]. Bearing in mind that 62

most of the current research on HPV integration had focused and established on the 63

pathological tissues. In clinical practice, cervical exfoliated cells might be collected 64

relatively at ease compared to pathological tissues, providing a distinct advantage to be 65

applied to generate HPV integration databases, and hence assessing the risks of HPV 66

3

integrations. To find out the regularity of HPV integration in cervical exfoliated cells 67

and also the correlation of HPV integration characteristics of exfoliated cells and 68

different degrees of cervical lesions, we deployed the cost-effective HIVID detection 69

technology. Altogether, this study had provided partial theoretical basis on whether 70

HPV integration events of cervical exfoliated cells could have potential to be regarded 71

as an effective clinical indicator. 72

2 Material and Method 73

A total of 230 HPV positive samples were obtained from the General Hospital of 74

the People's Liberation Army (PLA). All procedures performed in this study 75

involving human participants were in accordance with the ethical standards of the 76

institutional research committee and with the 1964 Helsinki Declaration and the later 77

amendments or comparable ethical standards. The study had been approved by the 78

Ethics Review Committee in the General Hospital of the PLA. HPV integration sites 79

were detected deploying HIVID method[10]. Functional annotation analysis was 80

performed using DAVID based on Gene Ontology and KEGG pathway databases [11, 81

12]. The categories of KEGG Pathways served as background databases. The 82

breakpoints were annotated through the latest ANNOVAR in hg19 coordinates [13]. 83

It is now documented that HPV integration could affect gene expression in following 84

aspects. 1. Influence flanking genes via cis-activation; 2. mimicking the effects of cis-85

acting enhancers to influence target genes over long distances[14, 15] (up to 1 Mb for 86

upstream enhancers and 850 kb for downstream enhancers). In this study, genes 87

located within a distance of <500kb away from breakpoints were regarded as the 88

affected genes, and being assessed in the HPV-positive samples[16]. 89

90

3 Results 91

3.1 Analysis of Integration Ratio and Breakpoint Number 92

The data analysis of these clinical samples suggested that the proportion of HPV 93

integrated samples and the average number of breakpoints in these samples positively 94

correlated with the stage of disease progression. The integration ratios of HPV infection, 95

4

CINI, CINII, CINIII, and cervical cancer were 32%,26%,40%,35%, and 77%, 96

respectively. The average breakpoint numbers of HPV infection, CINI, CINII, CINIII 97

and cervical cancer were 1.3, 1.4, 2, 1.8 and 3.7 respectively. As in the samples with 98

more advanced stages of the disease, the diversity of the HPV displayed a gradual 99

decease (Figure1). 100

3.2 The Recurrent Genes of HPV Integration in the DNA of Cervical Epithelial 101

Samples. 102

As documented in the frequency analysis, most genes only appeared once in the 103

samples, despite a number of recurrent genes (Figure2). Overall, 15 recurrent genes 104

(frequency = 2) were filtered out from the HPV positive cervical epithelial samples 105

(Table S1,Table S2). Pathway analysis revealed that the disrupted genes were 106

enriched in the pathway of Metabolism of xenobiotics by cytochrome P450, Chemical 107

carcinogenesis, Steroid hormone biosynthesis and so on (Table S3). 108

109

3.3 Distribution of Genetic Elements. 110

The characteristics of HPV breakpoints distribution had been surveyed. The results 111

revealed that HPV breakpoints were prone to the INTRON (P < 0.01, Chi-squared 112

test, Figure 3) and PROMOTER (P < 0.05, Chi-squared test, Figure 3) regions, but 113

not the INTERGENIC (P < 0.01, Chi-squared test, Figure 3) region. 114

115

4 Discussion 116

The cervical epithelial exfoliated cells had been widely used for early screening of 117

HPV, due to its obvious advantage of being non-invasive, which had greatly reduced 118

the incidence of cervical cancer. In spite of that the screening accuracy is yet to be 119

improved further. The development of new generation of HPV screening (enrich HPV 120

reads and localise HPV integration sites) had provided technical basis allowing the risk 121

assessment of cervical epithelial lesions. Having provided in the previous studies, 122

persistent HPV infection is the causal cause of cervical epithelial lesions, and the 123

occurrence of HPV integrations often indicating a greater risk of epithelial lesions [17, 124

5

18]. Herein, our results suggested that the proportion of HPV integrated samples and 125

the average number of breakpoints in the samples positively correlated with the stage 126

of disease progression. Further implying that certain categories of HPV integration 127

events could be good indicators of the progressive stage of developing cervical cancer. 128

In fact, detecting HPV integration of cervical epithelial cells has gradually been 129

practiced in clinical diagnosis and treatment. Generally speaking, for patients positive 130

for HPV high-risk infection and HPV integration, even with negative TCT, the patients 131

will be advised to carry out colposcopy examination, hence to prevent false diagnosis. 132

For patients positive for HPV high-risk infection, but negative for HPV integration and 133

TCT, the patients will be required to carry out short-term observation. In circumstances 134

where patients are positive for HPV high-risk infection and integration, and biopsy of 135

CINI, LEEP or cervical conization is usually recommended. For cervical cancer and 136

HPV integration positive patients, it is recommended to expand the scope of surgery 137

and increase the number of post-operative examinations. Furthermore, HPV integration 138

hotspots and the recurrent genes had also been filtered out. However, it is still unclear 139

whether the recurrent genes could be useful in terms of helping with prognosis. More 140

interestingly, the breakpoints are significantly enriched in the EXON and PROMOTER 141

regions. Therefore, it might be directly related to the disruption and alteration of gene 142

function[19, 20]. Gene pathway analysis results indicated that the HPV-integrated genes 143

were significantly inclined to the metabolic and steroid hormone bio-synthesis 144

pathways, and it is speculated that certain abnormalities in some of the metabolic and 145

bio-synthesis pathways may be affected contributing to the progression of cervical 146

cancer. In addition, HPV integrations had been evident to affect the cancer-associated 147

pathways and modify target gene expression in the host cells, which could further 148

promote carcinogenesis[21, 22]. Moreover, we have begun to conduct follow-up studies 149

on patients with HPV integration for future research. It will be necessary to further 150

determine the correlation of between disease progression and HPV integration. 151

Meanwhile, it will provide efficient means to evaluate disease progression. 152

In this study, deploying a genome-wide scanning method for HPV integrations had 153

6

enabled us to determine the close correlation between viral integration and clinical 154

disease progression. Our data had identified the inclination of HPV integration and the 155

recurrent HPV-integrated genes in cervical epithelial exfoliated cells which might be 156

useful in establishing a more sensitive and accurate future clinical application, helping 157

with the diagnosis of HPV positive cervical cancer. 158

159

160

FIG LEGEND: 161

162

163

Figure1 Clinical annotation of 230 samples. All panels are aligned with vertical tracks 164

representing 230 individuals. The data are sorted by the number of breakpoints, HPV 165

infection stage, CIN stage, Cancer and HPV type. 166

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167

Figure2 Gene frequency of HPV integration throughout the human genomes in 230 168

samples. Gene frequency of breakpoints across the human genome in 230 samples. 169

Each bar represents the sample frequency of HPV integration in the human genome 170

(hg19). Histogram axis units represent number of samples. Some loci with a high 171

frequency of integration are marked. 172

8

173

Figure3 Distribution of breakpoints in gene element region. The expected (assuming 174

uniform, random distribution, grey) and the observed (actual numbers, blue) ratio 175

of HPV breakpoints in Promoter, Exon, Intron, Intergenic region are shown. P values 176

were calculated by Chi-square test. 177

178

Supplementary Table 179

Table S1 HPV breakpoints in the cervical intraepithelial cells 180

Table S2 Table of gene frequency 181

Table S3 Analysis of Pathway 182

183

184

185

Acknowledgments 186

The study was funded by Cancer foundation of China (N2013016), Technology 187

Development Project of Medical and Health Science in Shandong Province (no. 188

2017WS516). 189

Authors’ Contributions 190

WYL, YQY and WPL conceived and wrote the paper. ST, PPW and YKZ analyzed 191

the data. 192

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193

Ethical Approval 194

All procedures performed in studies involving human participants were in accordance 195

with the ethical standards of the institutional research committee and with the 1964 196

Helsinki Declaration and its later amendments or comparable ethical standards. The 197

study had been approved by the Chinese PLA General Hospital. All subjects signed 198

written informed consent forms. 199

200

Competing Interests 201

202

The authors have declared that no competing interest exists. 203

204

205

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Supplementary Table 274

Table S1 HPV breakpoints in the cervical intraepithelial cells 275

Sample Number Chr Position Element Gene

18O003190_OC05

3_CapNGS

chrX 12709243 intronic FRMPD4

18O003190_OC05

3_CapNGS

chr3 95067171 intergenic LINC00879;MTHFD2P1

18O003140_OC05

3_CapNGS

chr6 21813214 ncRNA_intr

onic

CASC15

18O003140_OC05

3_CapNGS


onic

CASC15

18O003140_OC05

3_CapNGS


onic

CASC15

18O003122_OC05

3_CapNGS


onic

PVT1

18O003122_OC05

3_CapNGS


onic

PVT1

18O003122_OC05

3_CapNGS


onic

PVT1

18O003122_OC05

3_CapNGS


onic

PVT1

18O003105_OC05

3_CapNGS

chr13 97840226 intergenic LINC00456;MBNL2

18O003049_OC05

3_CapNGS

chr16 26066012 intronic HS3ST4

18O003049_OC05

3_CapNGS

chr10 4972497 intergenic AKR1C6P;AKR1C1

18O003049_OC05

3_CapNGS

chr10 5085051 intergenic AKR1C2;AKR1C3

18O002647_OC05

3_CapNGS

chr10 27282093 intergenic FAM238C;ANKRD26

18O002646_OC05

3_CapNGS

chr19 38585678 intronic SIPA1L3

18O002646_OC05

3_CapNGS

chr9 5090149 intronic JAK2

18O002646_OC05

3_CapNGS

chr7 110688995 intronic IMMP2L

18O002646_OC05

3_CapNGS


18O002646_OC05

3_CapNGS


18O002646_OC05

3_CapNGS


12

18O002646_OC05

3_CapNGS

chr3 60458039 intronic FHIT

18O002646_OC05

3_CapNGS

chr3 60450874 intronic FHIT

18O002646_OC05

3_CapNGS

chrX 96733527 intronic DIAPH2

18O002646_OC05

3_CapNGS


18O002645_OC05

3_CapNGS

chr2 42454188 intronic EML4

18O002645_OC05

3_CapNGS

chr13 74087557 intergenic KLF5;LINC00392

18O002606_OC05

3_CapNGS

chr6 124250180 intronic NKAIN2

18O002591_OC05

3_CapNGS

chr4 70616896 intronic SULT1B1

18O002587_OC05

3_CapNGS

chr17 29901935 upstream MIR365B;MIR4725

18O002585_OC05

3_CapNGS

chr12 57292061 intergenic HSD17B6;SDR9C7

18O002585_OC05

3_CapNGS

chr12 57292053 intergenic HSD17B6;SDR9C7

18O002463_OC05

3_CapNGS

chr3 189625657 intergenic TP63;P3H2

18O002463_OC05

3_CapNGS


18O002463_OC05

3_CapNGS


18O002431_OC05

3_CapNGS


onic

MIR1268A

18O002431_OC05

3_CapNGS


onic

MIR1268A

18O002431_OC05

3_CapNGS

chr2 146411850 intergenic TEX41;PABPC1P2

18O002387_OC05

3_CapNGS

chr5 160653448 intergenic LINC02159;GABRB2

18O002386_OC05

3_CapNGS

chr9 28147143 intronic LINGO2

18O002386_OC05

3_CapNGS

chr9 28147108 intronic LINGO2

18O002327_OC05

3_CapNGS

chr1 71327371 intronic PTGER3

18O002327_OC05

3_CapNGS

chrX 38978743 intergenic MID1IP1;LINC01281

13

18O002327_OC05

3_CapNGS

chr1 71272105 intergenic LINC01788;PTGER3

18O002245_OC05

3_CapNGS

chr2 142150724 intronic LRP1B

18O002245_OC05

3_CapNGS


18O002244_OC05

3_CapNGS

chr21 22859848 intronic NCAM2

18O002244_OC05

3_CapNGS

chr3 196773950 intronic DLG1

18O002186_OC05

3_CapNGS

chr9 93812640 intergenic SYK;LOC100129316

18O002186_OC05

3_CapNGS

chr5 74356497 intergenic LINC01336;ANKRD31

18O002174_OC05

3_CapNGS

chr1 27929435 intronic AHDC1

18O002174_OC05

3_CapNGS

chr1 27980139 intergenic FGR;IFI6

18O002174_OC05

3_CapNGS

chr1 27977931 intergenic FGR;IFI6

18O001816_OC05

3_CapNGS

chr2 214516172 intronic SPAG16

18O001816_OC05

3_CapNGS


18O001816_OC05

3_CapNGS


18O001816_OC05

3_CapNGS

chr2 214055740 intergenic LINC01953;LOC10013045

1

18O001804_OC05

3_CapNGS


onic

ANKRD30BL

18O001804_OC05

3_CapNGS

chr5 134372585 intronic C5orf66

18O000720_OC05

3_CapNGS

chr2 183273384 intronic PDE1A

18O000687_OC05

3_CapNGS

chr3 96685606 intronic EPHA6

18O000687_OC05

3_CapNGS

chr3 96685601 intronic EPHA6

18O000687_OC05

3_CapNGS

chr10 37554874 intergenic ANKRD30A;LINC00993

18O000683_OC05

3_CapNGS

chrX 49755402 intronic CLCN5

18O000664_OC05

3_CapNGS


onic

LOC100288778

14

18O000664_OC05

3_CapNGS

chr2 114341255 ncRNA_exon

ic

WASH2P

18O000664_OC05

3_CapNGS

chr3 188839421 intergenic TPRG1-AS1;TPRG1

18O000664_OC05

3_CapNGS

chr19 39540562 intergenic FBXO27;ACP7

18O000595_OC05

3_CapNGS


18O000595_OC05

3_CapNGS

chr6 30405337 intergenic TRIM39-RPP21;HLA-E

18O000595_OC05

3_CapNGS

chr2 192064246 intergenic STAT4;MYO1B

18O000574_OC05

3_CapNGS

chr3 138884153 intergenic BPESC1;PISRT1

18O000559_OC05

3_CapNGS

chr8 62160883 intergenic LOC100130298;CLVS1

18O000559_OC05

3_CapNGS


18O000559_OC05

3_CapNGS


18O000559_OC05

3_CapNGS

chr2 180965327 intergenic CWC22;SCHLAP1

18O000494_OC05

3_CapNGS

chr5 147485766 intronic SPINK5

18O000494_OC05

3_CapNGS

chr7 34185663 intronic BMPER

18O000480_OC05

3_CapNGS

chr9 88873831 intronic C9orf153

18O000480_OC05

3_CapNGS

chrX 11887810 intergenic MSL3;FRMPD4

18O000480_OC05

3_CapNGS

chr4 17244871 intergenic LINC02493;SNORA75B

18O000467_OC05

3_CapNGS

chrX 152119166 intronic ZNF185

18O000467_OC05

3_CapNGS

chr3 158529525 intronic MFSD1

18O000467_OC05

3_CapNGS

chrX 152042006 intergenic NSDHL;ZNF185

18O000418_OC05

3_CapNGS

chr7 1280995 intergenic UNCX;MICALL2

18O000412_OC05

3_CapNGS

chr10 44600364 intergenic LINC00841;C10orf142

18O000408_OC05

3_CapNGS

chr5 102166734 intronic PAM

15

18O000404_OC05

3_CapNGS

chr3 67606170 intronic SUCLG2

18O000404_OC05

3_CapNGS

chr8 129242878 intergenic MIR1208;LINC00824

18O000404_OC05

3_CapNGS

chr2 64030360 intergenic MDH1;UGP2

18O000360_OC05

3_CapNGS

chr10 105720651 intergenic STN1;SLK

18O000337_OC05

3_CapNGS

chr4 87566760 intronic PTPN13

18O000336_OC05

3_CapNGS

chr2 50913806 intronic NRXN1

18O000336_OC05

3_CapNGS


18O000336_OC05

3_CapNGS


18O000336_OC05

3_CapNGS


18O000257_OC05

3_CapNGS

chr13 83400904 intergenic LINC00564;SLITRK1

18O000210_OC05

3_CapNGS

chr16 1363414 intronic UBE2I

18O000210_OC05

3_CapNGS


18O000210_OC05

3_CapNGS


18O000209_OC05

3_CapNGS

chr22 28423456 intronic TTC28

18O000209_OC05

3_CapNGS

chr17 28749622 intronic CPD

18O000209_OC05

3_CapNGS

chr1 195092056 intergenic LINC01031;LINC01724

18O000198_OC05

3_CapNGS

chr17 39738664 UTR3 KRT14

18O000197_OC05

3_CapNGS

chr4 142965708 intronic INPP4B

18O000197_OC05

3_CapNGS

chr4 142961049 intronic INPP4B

18O000045_OC05

3_CapNGS

chr9 139743600 UTR5 PHPT1

18O000045_OC05

3_CapNGS

chr6 20915150 intronic CDKAL1

18O000045_OC05

3_CapNGS

chr14 99287089 intergenic C14orf177;BCL11B

16

18O000045_OC05

3_CapNGS

chr9 139743883 exonic PHPT1

17O011808_OC05

3_CapNGS

chr4 151085095 intronic DCLK2

17O011808_OC05

3_CapNGS

chr1 142934469 intergenic ANKRD20A12P;LOC102723

769

17O011808_OC05

3_CapNGS

chr1 142934159 intergenic ANKRD20A12P;LOC102723

769

17O011795_OC05

3_CapNGS

chr5 52636606 intergenic LOC257396;FST

17O011795_OC05

3_CapNGS

chr5 52619266 intergenic LOC257396;FST

17O011720_OC05

3_CapNGS

chr15 59794826 intronic FAM81A

17O011720_OC05

3_CapNGS

chr15 59960896 intronic BNIP2

17O011720_OC05

3_CapNGS

chr15 59960893 intronic BNIP2

17O011719_OC05

3_CapNGS


onic

MIR4527HG

17O011684_OC05

3_CapNGS

chr6 135498935 intergenic HBS1L;MYB

17O011684_OC05

3_CapNGS

chr6 135498904 intergenic HBS1L;MYB

17O011637_OC05

3_CapNGS


3

17O011636_OC05

3_CapNGS

chr5 35865694 intronic IL7R

17O011577_OC05

3_CapNGS

chr3 122308537 intronic PARP15

17O011577_OC05

3_CapNGS

chr8 127623005 intergenic FAM84B;PCAT1

17O011576_OC05

3_CapNGS

chr20 19938991 intronic RIN2

17O011576_OC05

3_CapNGS

chr20 19988082 intergenic RIN2;NAA20

17O011575_OC05

3_CapNGS

chrX 66538204 intergenic EDA2R;AR

17O011575_OC05

3_CapNGS

chrX 66538197 intergenic EDA2R;AR

17O011573_OC05

3_CapNGS

chr12 11544572 UTR3 PRB2

17O011573_OC05

3_CapNGS

chr2 22856719 intergenic LINC01884;KLHL29

17

17O011572_OC05

3_CapNGS

chr20 61840316 intronic YTHDF1

17O011571_OC05

3_CapNGS

chr20 61840317 intronic YTHDF1

17O011559_OC05

3_CapNGS

chr3 128079337 intronic EEFSEC

17O011559_OC05

3_CapNGS


17O011559_OC05

3_CapNGS


17O011559_OC05

3_CapNGS


17O011556_OC05

3_CapNGS

chr8 141528265 intergenic CHRAC1;AGO2

17O011556_OC05

3_CapNGS

chr8 141528242 downstream CHRAC1

17O011555_OC05

3_CapNGS

chr3 37904951 intronic CTDSPL

17O011555_OC05

3_CapNGS

chr18 57794431 intergenic PMAIP1;MC4R

17O011555_OC05

3_CapNGS

chr12 75245572 intergenic ATXN7L3B;KCNC2

17O011540_OC05

3_CapNGS

chr17 37849833 intronic ERBB2

17O011540_OC05

3_CapNGS

chr17 37849831 intronic ERBB2

17O011540_OC05

3_CapNGS

chr1 243967416 intronic AKT3

17O011515_OC05

3_CapNGS

chr16 33959885 intergenic ENPP7P13;LINC00273

17O011515_OC05

3_CapNGS

chr2 133022750 intergenic ANKRD30BL;ZNF806

17O011478_OC05

3_CapNGS

chr10 135333161 intergenic SCART1;CYP2E1

17O011478_OC05

3_CapNGS

chr10 134612044 intergenic NKX6-2;CFAP46

17O011426_OC05

3_CapNGS

chr9 112176212 intronic PTPN3

17O011426_OC05

3_CapNGS

chr11 93672443 intergenic VSTM5;HEPHL1

17O011426_OC05

3_CapNGS

chr3 194200246 intergenic ATP13A3;LINC00884

17O011426_OC05

3_CapNGS

chr15 45814280 exonic SLC30A4

18

17O011230_OC05

3_CapNGS


onic

WTAPP1

17O011230_OC05

3_CapNGS

chr11 102739914 intronic MMP12

17O011228_OC05

3_CapNGS

chr4 172351833 intergenic MIR6082;LINC02174

17O011155_OC05

3_CapNGS


17O011154_OC05

3_CapNGS

chr15 71965928 intronic THSD4

17O011153_OC05

3_CapNGS

chrX 111377331 intronic RTL4

17O011153_OC05

3_CapNGS

chrX 138636032 intronic F9

17O011153_OC05

3_CapNGS

chrX 138636027 intronic F9

17O011153_OC05

3_CapNGS

chrX 138661710 intergenic F9;MCF2

17O011153_OC05

3_CapNGS

chrX 138661705 intergenic F9;MCF2

17O011151_OC05

3_CapNGS

chr14 26036012 intergenic STXBP6;NOVA1

17O011151_OC05

3_CapNGS

chr17 46833787 intergenic HOXB13;TTLL6

17O011137_OC05

3_CapNGS

chr20 36780798 intronic TGM2

17O011137_OC05

3_CapNGS


17O011137_OC05

3_CapNGS


17O011105_OC05

3_CapNGS

chr17 66691396 intergenic LINC01482;ABCA8

17O011102_OC05

3_CapNGS

chr2 191462814 intergenic NEMP2;NAB1

17O011102_OC05

3_CapNGS


17O011102_OC05

3_CapNGS


17O011102_OC05

3_CapNGS


17O010971_OC05

3_CapNGS

chr2 109387815 intronic RANBP2

17O010971_OC05

3_CapNGS

chr21 16369512 intronic NRIP1

19

17O010971_OC05

3_CapNGS

chr2 155661855 intronic KCNJ3

17O010971_OC05

3_CapNGS

chr16 65303923 intergenic LINC02126;LINC00922

17O010969_OC05

3_CapNGS

chr19 45461468 intronic CLPTM1

17O010969_OC05

3_CapNGS

chr19 45248164 intergenic CEACAM16;BCL3

17O010969_OC05

3_CapNGS

chr19 45245817 intergenic CEACAM16;BCL3

17O010969_OC05

3_CapNGS

chr19 45452947 downstream APOC2;APOC4-APOC2

17O010945_OC05

3_CapNGS

chr3 116290632 intergenic LINC00903;TUSC7

17O010903_OC05

3_CapNGS

chr11 69042647 intergenic LOC338694;MYEOV

17O010903_OC05

3_CapNGS

chr15 33502979 intergenic FMN1;TMCO5B

17O010355_OC05

3_CapNGS

chr8 119582719 intronic SAMD12

17O010289_OC05

3_CapNGS

chr2 228222208 UTR3 MFF

17O010289_OC05

3_CapNGS

chr2 228220599 intronic MFF

17O010289_OC05

3_CapNGS

chr10 42599832 intergenic NONE;LOC441666

17O010289_OC05

3_CapNGS

chr10 42599827 intergenic NONE;LOC441666

17O010288_OC05

3_CapNGS

chr6 114994918 intergenic HDAC2-

AS2;LOC105377962

17O010150_OC05

3_CapNGS

chr1 244632838 intronic CATSPERE

17O010150_OC05

3_CapNGS


17O010150_OC05

3_CapNGS


17O010148_OC05

3_CapNGS

chr6 144661706 intronic UTRN

17O010141_OC05

3_CapNGS

chr4 94500527 intronic GRID2

17O010136_OC05

3_CapNGS

chr2 178091891 intergenic HNRNPA3;NFE2L2

17O010136_OC05

3_CapNGS

chr2 178091890 intergenic HNRNPA3;NFE2L2

20

17O010136_OC05

3_CapNGS

chr2 178094767 downstream NFE2L2

17O010116_OC05

3_CapNGS

chr1 55463866 upstream BSND

17O010116_OC05

3_CapNGS

chr1 55463862 upstream BSND

17O010116_OC05

3_CapNGS


onic

ZNF670-ZNF695

17O010116_OC05

3_CapNGS

chr1 55470534 intronic BSND

17O010116_OC05

3_CapNGS

chr4 149889425 intergenic LOC105377480;LINC0235

5

17O010116_OC05

3_CapNGS


5

17O010116_OC05

3_CapNGS


5

17O010116_OC05

3_CapNGS


5

17O010116_OC05

3_CapNGS

chr1 55484461 intergenic BSND;PCSK9

17O010116_OC05

3_CapNGS


17O010116_OC05

3_CapNGS


17O010116_OC05

3_CapNGS


17O010076_OC05

3_CapNGS

chr2 48733104 intronic PPP1R21

17O010076_OC05

3_CapNGS

chr2 48733071 intronic PPP1R21

17O004089_OC05

3_CapNGS

chr1 209556772 intergenic LINC01698;MIR205HG

17O004089_OC05

3_CapNGS


17O004089_OC05

3_CapNGS


17O004089_OC05

3_CapNGS


17O004089_OC05

3_CapNGS


17O003975_OC05

3_CapNGS

chr3 160505662 intronic PPM1L

17O003975_OC05

3_CapNGS

chr10 14189084 intronic FRMD4A

21

17O003947_OC05

3_CapNGS

chr11 18015042 intronic SERGEF

17O003946_OC05

3_CapNGS

chr2 159762187 intergenic DAPL1;TANC1

17O003943_OC05

3_CapNGS


onic

RNF219-AS1

17O003942_OC05

3_CapNGS

chr6 7109779 intronic RREB1

17O003942_OC05

3_CapNGS

chr6 7108893 intronic RREB1

17O003942_OC05

3_CapNGS

chr10 121512527 intronic INPP5F

17O003942_OC05

3_CapNGS

chr10 121512526 intronic INPP5F

17O003942_OC05

3_CapNGS

chr2 79409756 intergenic REG3A;LOC101927987

17O003942_OC05

3_CapNGS

chr10 121243601 intergenic GRK5;RGS10

17O003940_OC05

3_CapNGS

chr4 74719426 intronic PF4V1

17O003940_OC05

3_CapNGS

chr17 55987808 intronic CUEDC1

17O003940_OC05

3_CapNGS


17O003940_OC05

3_CapNGS


17O003940_OC05

3_CapNGS


17O003940_OC05

3_CapNGS


5

17O003940_OC05

3_CapNGS


5

17O003775_OC05

3_CapNGS

chrX 129473674 upstream SLC25A14

17O003694_OC05

3_CapNGS

chr2 83219955 intergenic DHFRP3

17O003682_OC05

3_CapNGS

chr3 169037256 intronic MECOM

17O003682_OC05

3_CapNGS


17O003682_OC05

3_CapNGS


17O003682_OC05

3_CapNGS


22

17O003682_OC05

3_CapNGS


17O003678_OC05

3_CapNGS


onic

LOC101928438

17O003678_OC05

3_CapNGS

chr9 102720177 intronic STX17

17O003678_OC05

3_CapNGS

chr9 102720173 intronic STX17

17O003678_OC05

3_CapNGS

chr9 102606231 intronic NR4A3

17O003678_OC05

3_CapNGS


17O003678_OC05

3_CapNGS


17O003675_OC05

3_CapNGS

chr1 209492679 intergenic PLXNA2

17O003675_OC05

3_CapNGS

chr1 209514220 intergenic LINC01696

17O003646_OC05

3_CapNGS

chr8 54140249 UTR3 OPRK1

17O003646_OC05

3_CapNGS

chr8 54140247 UTR3 OPRK1

17O003646_OC05

3_CapNGS

chr19 41353770 intronic CYP2A6

17O003646_OC05

3_CapNGS

chr4 100261545 intronic ADH1C

17O003646_OC05

3_CapNGS

chr8 54136836 intergenic NPBWR1

17O003646_OC05

3_CapNGS

chr19 41347849 intergenic CYP2T1P

17O003646_OC05

3_CapNGS

chr2 62492040 intergenic B3GNT2

17O003646_OC05

3_CapNGS

chr2 62492035 intergenic B3GNT2

17O003646_OC05

3_CapNGS

chr4 100256222 intergenic ADH1B

17O003645_OC05

3_CapNGS

chr8 11556107 intronic GATA4

17O003645_OC05

3_CapNGS

chr18 58909497 intergenic MC4R

17O003557_OC05

3_CapNGS

chr9 14392011 intronic NFIB

17O003557_OC05

3_CapNGS


23

17O003557_OC05

3_CapNGS


17O003557_OC05

3_CapNGS


17O003557_OC05

3_CapNGS


17O003557_OC05

3_CapNGS


17O003557_OC05

3_CapNGS


17O003557_OC05

3_CapNGS


17O003557_OC05

3_CapNGS


17O003557_OC05

3_CapNGS


17O003557_OC05

3_CapNGS


17O003557_OC05

3_CapNGS


17O003557_OC05

3_CapNGS


17O003557_OC05

3_CapNGS

chr19 15630073 intronic CYP4F22

17O003557_OC05

3_CapNGS

chr19 15625131 intronic CYP4F22

17O003557_OC05

3_CapNGS

chr19 15617067 intergenic PGLYRP2

17O003557_OC05

3_CapNGS

chr9 14444237 intergenic NFIB

17O003557_OC05

3_CapNGS

chr9 14425226 intergenic NFIB

17O003557_OC05

3_CapNGS

chr2 178138311 intergenic NFE2L2

17O003557_OC05

3_CapNGS

chr19 15750544 intergenic CYP4F8

17O003555_OC05

3_CapNGS


onic

KCCAT333

17O003555_OC05

3_CapNGS

chr7 17393615 intergenic AHR

17O003555_OC05

3_CapNGS

chr7 17393612 intergenic AHR

17O003511_OC05

3_CapNGS

chr3 189576796 intronic TP63

24

17O003511_OC05

3_CapNGS

chr3 189576794 intronic TP63

17O003511_OC05

3_CapNGS

chr3 189710101 intronic P3H2

17O002698_OC05

3_CapNGS

chr19 56161395 intronic CCDC106

17O002698_OC05

3_CapNGS

chr13 73788866 intergenic KLF5

17O000585_OC05

3_CapNGS

chr3 96077123 intergenic MTHFD2P1

17O000583_OC05

3_CapNGS

chr10 75386316 intergenic USP54

17O000583_OC05

3_CapNGS

chr10 4083087 intergenic MIR6078

17O000582_OC05

3_CapNGS

chr1 38467812 intronic FHL3

17O000582_OC05

3_CapNGS


17O000582_OC05

3_CapNGS


17O000582_OC05

3_CapNGS


17O000582_OC05

3_CapNGS


17O000579_OC05

3_CapNGS

chr7 5316359 intergenic WIPI2

17O000579_OC05

3_CapNGS

chr7 5316320 intergenic WIPI2

17O000579_OC05

3_CapNGS

chr3 195552510 intergenic MUC4

17O000577_OC05

3_CapNGS


17O000577_OC05

3_CapNGS


276

277

278

279

280

281

282

25

Table S2 Table of gene frequency 283

Gene Frequency

P3H2 2

MC4R 2

KLF5 2

FRMPD4 2

NR4A3 2

PABPC1P2 2

TEX41 2

DIAPH2 2

LRP1B 2

ANKRD30BL 2

TP63 2

MTHFD2P1 2

YTHDF1 2

NFE2L2 2

MECOM 2

ATXN7L3B 1

KCCAT333 1

C5orf66 1

SYK 1

HDAC2-AS2 1

PTGER3 1

IL7R 1

AKR1C3 1

NAB1 1

RIN2 1

WTAPP1 1

DLG1 1

CLVS1 1

MCF2 1

PISRT1 1

EDA2R 1

LINC01482 1

INPP5F 1

CYP2A6 1

LINC01239 1

ZNF185 1

ABCA8 1

FMN1 1

LINC00273 1

MYO1B 1

PCAT1 1

26

PGLYRP2 1

SUCLG2 1

AHDC1 1

NKAIN2 1

FAM238C 1

TchrD4 1

LINGO2 1

ATP13A3 1

PAM 1

LINC01788 1

LINC00884 1

EML4 1

KRT14 1

MBNL2 1

DHFRP3 1

PARP15 1

EPHA6 1

ACP7 1

MIR6078 1

CLPTM1 1

LOC100288778 1

PHPT1 1

CEACAM16 1

LOC101929563 1

LOC338694 1

NEMP2 1

SDR9C7 1

MIR205HG 1

SCHLAP1 1

PVT1 1

MIR1208 1

LINC00903 1

SERGEF 1

STN1 1

CYP2T1P 1

NAA20 1

LINC01281 1

LOC100130298 1

MID1IP1 1

NPBWR1 1

UNCX 1

SLITRK1 1

FGR 1

ANKRD26 1

27

FHL3 1

chr3ST4 1

F9 1

FST 1

ADH1B 1

IMMP2L 1

AKR1C1 1

NRXN1 1

AGO2 1

LINC01698 1

SCART1 1

RANBP2 1

FRMD4A 1

STAT4 1

MIR1268A 1

PLXNA2 1

BCL11B 1

REG3A 1

TPRG1 1

HBS1L 1

MUC4 1

LINC02355 1

LINC01724 1

LINC02174 1

WASH2P 1

ANKRD20A12P 1

LINC02159 1

LINC00841 1

LOC339298 1

SULT1B1 1

CPD 1

FAM81A 1

TPRG1-AS1 1

NRIP1 1

SLC25A14 1

AR 1

BNIP2 1

ZNF806 1

MIR4725 1

MFSD1 1

CWC22 1

EEFSEC 1

GRID2 1

CATSPERE 1

28

CYP4F22 1

LINC00456 1

HNRNPA3 1

DCLK2 1

BPESC1 1

STX17 1

PCSK9 1

PMAIP1 1

LINC00564 1

INPP4B 1

MIR365B 1

RGS10 1

PPM1L 1

KCNJ3 1

GABRB2 1

C9orf153 1

FHIT 1

TGM2 1

LINC01031 1

SLK 1

OPRK1 1

ZNF670-ZNF695 1

JAK2 1

PTPN3 1

HOXB13 1

NKX6-2 1

IFI6 1

UGP2 1

PRB2 1

PTPN13 1

MSL3 1

UTRN 1

LOC102723769 1

AKT3 1

TRIM39-RPP21 1

CDKAL1 1

TANC1 1

DAPL1 1

BMPER 1

AKR1C6P 1

TMCO5B 1

ANKRD30A 1

CYP4F8 1

CUEDC1 1

29

SPAG16 1

chrD17B6 1

LOC101928438 1

LINC00922 1

SAMD12 1

ANKRD31 1

CCDC106 1

LINC00824 1

GRK5 1

NOVA1 1

LINC00879 1

AKR1C2 1

ENPP7P13 1

KCNC2 1

FBXO27 1

C10orf142 1

LINC00993 1

PDE1A 1

LINC01336 1

WIPI2 1

HEPHL1 1

MIR4527HG 1

APOC4-APOC2 1

CFAP46 1

LOC257396 1

LINC01568 1

RTL4 1

LINC02493 1

MMP12 1

NFIB 1

APOC2 1

C14orf177 1

MIR6082 1

SIPA1L3 1

GATA4 1

TTLL6 1

LOC105377480 1

LINC01953 1

NSDHL 1

RREB1 1

MFF 1

ADH1C 1

MICALL2 1

MDH1 1

30

CASC15 1

BCL3 1

PF4V1 1

LINC01696 1

MYEOV 1

STXBP6 1

PPP1R21 1

LOC100130451 1

CHRAC1 1

UBE2I 1

AHR 1

B3GNT2 1

NCAM2 1

LOC101928035 1

FAM84B 1

LINC00392 1

CLCN5 1

RNF219-AS1 1

CYP2E1 1

LINC01898 1

TTC28 1

LINC01884 1

LOC101927987 1

CTDSPL 1

BSND 1

SNORA75B 1

LOC105377962 1

LOC100129316 1

LINC02126 1

USP54 1

SPINK5 1

HLA-E 1

KLHL29 1

SLC30A4 1

TUSC7 1

VSTM5 1

MYB 1

ERBB2 1

284

285

the characteristics of hpv integration in cervical …1 1 the characteristics of hpv integration in...

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