Label-free cervicovaginal fluid proteome profiling reflects the cervix neoplastic transformation

Nature of the Association between Rheumatoid Arthritis and Cervical Cancer and Its Potential Therapeutic Implications

It is now established that patients with rheumatoid arthritis (RA) have an increased risk of developing cervical cancer (CC) or its precursor, cervical intraepithelial neoplasia (CIN). However, the underlying mechanisms of this association have not been elucidated. RA is characterized by unresolved chronic inflammation. It is suggested that human papillomavirus (HPV) infection in RA patients exacerbates inflammation, increasing the risk of CC. The tumor microenvironment in RA patients with CC is also marked by chronic inflammation, which aggravates the manifestations of both conditions. Gut and vaginal dysbiosis are also considered potential mechanisms that contribute to the chronic inflammation and aggravation of RA and CC manifestations. Numerous clinical and pre-clinical studies have demonstrated the beneficial effects of various nutritional approaches to attenuate chronic inflammation, including polyunsaturated fatty acids and their derivatives, specialized pro-resolving mediators (SPMs), probiotics, prebiotics, and certain diets. We believe that successful resolution of chronic inflammation and correction of dysbiosis, in combination with current anti-RA and anti-CC therapies, is a promising therapeutic approach for RA and CC. This approach could also reduce the risk of CC development in HPV-infected RA patients.

Clinical application of serum-based proteomics technology in human tumor research

The rapid development of proteomics technology in the past decades has led to further human understanding of tumor research, and in some ways, the technology plays a very important supporting role in the early detection of tumors. Human serum has been shown to contain a variety of proteins closely related to life activities, and the dynamic change in proteins can often reflect the physiological and pathological conditions of the body. Serum has the advantage of easy extraction, so the application of proteomics technology in serum has become a hot spot and frontier area for the study of malignant tumors. However, there are still many difficulties in the standardized use of proteomic technologies, which inevitably limit the clinical application of proteomic technologies due to the heterogeneity of human proteins leading to incomplete whole proteome populations, in addition to most serum protein markers being now not highly specific in aiding the early detection of tumors. Nevertheless, further development of proteomics technologies will greatly increase our understanding of tumor biology and help discover more new tumor biomarkers with specificity that will enable medical technology.

Chemical Barrier Proteins in Human Body Fluids

Chemical barriers are composed of those sites of the human body where potential pathogens can contact the host cells. A chemical barrier is made up by different proteins that are part of the antimicrobial and immunomodulatory protein/peptide (AMP) family. Proteins of the AMP family exert antibacterial, antiviral, and/or antifungal activity and can modulate the immune system. Besides these proteins, a wide range of proteases and protease inhibitors can also be found in the chemical barriers maintaining a proteolytic balance in the host and/or the pathogens. In this review, we aimed to identify the chemical barrier components in nine human body fluids. The interaction networks of the chemical barrier proteins in each examined body fluid were generated as well.

Insights on Proteomics-Driven Body Fluid-Based Biomarkers of Cervical Cancer

Cervical cancer is one of the top malignancies in women around the globe, which still holds its place despite being preventable at early stages. Gynecological conditions, even maladies like cervical cancer, still experience scrutiny from society owing to prevalent taboo and invasive screening methods, especially in developing economies. Additionally, current diagnoses lack specificity and sensitivity, which prolong diagnosis until it is too late. Advances in omics-based technologies aid in discovering differential multi-omics profiles between healthy individuals and cancer patients, which could be utilized for the discovery of body fluid-based biomarkers. Body fluids are a promising potential alternative for early disease detection and counteracting the problems of invasiveness while also serving as a pool of potential biomarkers. In this review, we will provide details of the body fluids-based biomarkers that have been reported in cervical cancer. Here, we have presented our perspective on proteomics for global biomarker discovery by addressing several pertinent problems, including the challenges that are confronted in cervical cancer. Further, we also used bioinformatic methods to undertake a meta-analysis of significantly up-regulated biomolecular profiles in CVF from cervical cancer patients. Our analysis deciphered alterations in the biological pathways in CVF such as immune response, glycolytic processes, regulation of cell death, regulation of structural size, protein polymerization disease, and other pathways that can cumulatively contribute to cervical cancer malignancy. We believe, more extensive research on such biomarkers, will speed up the road to early identification and prevention of cervical cancer in the near future.

Prognostic utility of the ovarian cancer secretome: a systematic investigation

BACKGROUND

Ovarian cancer is usually detected at an advanced stage with frequent recurrence. The recurrence-free survival and overall survival is influenced by the age at diagnosis, tumor stage and histological subtype. Nonetheless, quantifiable prognostic biomarkers are needed for early identification of the high-risk patients and for personalized medicine. Several studies link tumor-specific dysregulated expression of certain proteins with ovarian cancer prognosis. However, careful investigation of presence of these prognostically relevant proteins in ovarian cancer secretome is lacking.

OBJECTIVE

To critically analyze the recent published data on prognostically relevant proteins for ovarian cancer and to carefully search how many of them are reported in the published ovarian cancer secretome datasets.

DESIGN

A search for relevant studies in the past 2 years was conducted in PubMed and a comprehensive list of proteins associated with the ovarian cancer prognosis was prepared. These were cross-referred to the published ovarian cancer secretome profiles. The proteins identified in the secretome were further shortlisted based on a scoring strategy employing stringent criteria.

RESULTS

A panel of seven promising secretory biomarkers associated with ovarian cancer prognosis is proposed.

CONCLUSION

Scanning the ovarian cancer secretome datasets provides the opportunity to identify if tumor-specific biomarkers could be tested as secretory biomarkers. Detecting their levels in the body fluid would be more advantageous than evaluating the expression in the tissue, since it could be monitored multiple times over the course of the disease to have a better judgment of the prognosis and response to therapy.

Changes in the Proteome in the Development of Chronic Human Papillomavirus Infection-A Prospective Study in HIV Positive and HIV Negative Rwandan Women

BACKGROUND

Effects on the proteome when a high risk (HR)-HPV infection occurs, when it is cleared and when it becomes chronic were investigated. Moreover, biomarker panels that could identify cervical risk lesions were assessed.

METHODS

Cytology, HPV screening and proteomics were performed on cervical samples from Rwandan HIV+ and HIV- women at baseline, at 9 months, at 18 months and at 24 months. Biological pathways were identified using the String database.

RESULTS

The most significantly affected pathway when an incident HR-HPV infection occurred was neutrophil degranulation, and vesicle-mediated transport was the most significantly affected pathway when an HR-HPV infection was cleared; protein insertion into membrane in chronic HR-HPV lesions and in lesions where HR-HPVs were cleared were compared; and cellular catabolic process in high-grade lesions was compared to that in negative lesions. A four-biomarker panel (EIF1; BLOC1S5; LIMCH1; SGTA) was identified, which was able to distinguish chronic HR-HPV lesions from cleared HR-HPV/negative lesions (sensitivity 100% and specificity 91%). Another four-biomarker panel (ERH; IGKV2-30; TMEM97; DNAJA4) was identified, which was able to distinguish high-grade lesions from low-grade/negative lesions (sensitivity 100% and specificity 81%).

CONCLUSIONS

We have identified the biological pathways triggered in HR-HPV infection, when HR-HPV becomes chronic and when cervical risk lesions develop. Moreover, we have identified potential biomarkers that may help to identify women with cervical risk lesions.

HBFP: a new repository for human body fluid proteome

Body fluid proteome has been intensively studied as a primary source for disease biomarker discovery. Using advanced proteomics technologies, early research success has resulted in increasingly accumulated proteins detected in different body fluids, among which many are promising biomarkers. However, despite a handful of small-scale and specific data resources, current research is clearly lacking effort compiling published body fluid proteins into a centralized and sustainable repository that can provide users with systematic analytic tools. In this study, we developed a new database of human body fluid proteome (HBFP) that focuses on experimentally validated proteome in 17 types of human body fluids. The current database archives 11 827 unique proteins reported by 164 scientific publications, with a maximal false discovery rate of 0.01 on both the peptide and protein levels since 2001, and enables users to query, analyze and download protein entries with respect to each body fluid. Three unique features of this new system include the following: (i) the protein annotation page includes detailed abundance information based on relative qualitative measures of peptides reported in the original references, (ii) a new score is calculated on each reported protein to indicate the discovery confidence and (iii) HBFP catalogs 7354 proteins with at least two non-nested uniquely mapping peptides of nine amino acids according to the Human Proteome Project Data Interpretation Guidelines, while the remaining 4473 proteins have more than two unique peptides without given sequence information. As an important resource for human protein secretome, we anticipate that this new HBFP database can be a powerful tool that facilitates research in clinical proteomics and biomarker discovery.

Database URL:https://bmbl.bmi.osumc.edu/HBFP/

Molecular markers for cervical cancer screening

INTRODUCTION

Cervical cancer remains a significant healthcare problem, notably in low- to middle-income countries. While a negative test for hrHPV has a predictive value of more than 99.5%, its positive predictive value is less than 10% for CIN2+ stages. This makes the use of a so-called triage test indispensable for population-based screening to avoid referring women, that are ultimately at low risk of developing cervical cancer, to a gynecologist. This review will give an overview of tests that are based on epigenetic marker panels and protein markers.

AREAS COVERED

There is a medical need for molecular markers with a better predictive value to discriminate hrHPV-positive women that are at risk of developing cervical cancer from those that are not. Areas covered are epigenetic and protein markers as well as health economic considerations in view of the fact that most cases of cervical cancer arise in low-to-middle-income countries.

EXPERT OPINION

While there are biomarker assays based on changes at the nucleic acid (DNA methylation patterns, miRNAs) and at the protein level, they are not widely used in population screening. Combining nucleic acid-based and protein-based tests could improve the overall specificity for discriminating CIN2+ lesions that carry a low risk of progressing to cervical cancer within the screening interval from those that carry an elevated risk. The challenge is to reduce unnecessary referrals without an undesired increase in false-negative diagnoses resulting in cases of cervical cancer that could have been prevented. A further challenge is to develop tests for low-and middle-income countries, which is critical to reduce the worldwide burden of cervical cancer.

Comprehensive Library Generation for Identification and Quantification of Endometrial Cancer Protein Biomarkers in Cervico-Vaginal Fluid

Simple Summary

Endometrial cancer is the most common cancer of the female reproductive tract, and its incidence is rising. Early diagnosis has the potential to improve survival as women can receive care at the earliest possible stage when curative treatment is likely. Current tests for endometrial cancer diagnosis are sequentially invasive with low patient acceptability. A detection tool based on minimally invasive samples such as cervico-vaginal fluid would be a major advance in the field. This study focuses on the potential of detecting endometrial cancer based on the proteins and peptides expressed in cervico-vaginal fluid. Using Sequential window acquisition of all theoretical mass spectra (SWATH-MS), we present a spectral library of thousands of proteins in the cervico-vaginal fluid of women with or at risk of endometrial cancer. This important resource will enable the identification of endometrial cancer biomarkers in cervico-vaginal fluid and advances our knowledge of the role of proteomics in endometrial cancer detection.

Abstract

Endometrial cancer is the most common gynaecological malignancy in high-income countries and its incidence is rising. Early detection, aided by highly sensitive and specific biomarkers, has the potential to improve outcomes as treatment can be provided when it is most likely to effect a cure. Sequential window acquisition of all theoretical mass spectra (SWATH-MS), an accurate and reproducible platform for analysing biological samples, offers a technological advance for biomarker discovery due to its reproducibility, sensitivity and potential for data re-interrogation. SWATH-MS requires a spectral library in order to identify and quantify peptides from multiplexed mass spectrometry data. Here we present a bespoke spectral library of 154,206 transitions identifying 19,394 peptides and 2425 proteins in the cervico-vaginal fluid of postmenopausal women with, or at risk of, endometrial cancer. We have combined these data with a library of over 6000 proteins generated based on mass spectrometric analysis of two endometrial cancer cell lines. This unique resource enables the study of protein biomarkers for endometrial cancer detection in cervico-vaginal fluid. Data are available via ProteomeXchange with unique identifier PXD025925.

miRNAs and Their Gene Targets-A Clue to Differentiate Pregnancies with Small for Gestational Age Newborns, Intrauterine Growth Restriction, and Preeclampsia

Despite the differences in the clinical manifestations of major obstetric syndromes, such as preeclampsia (PE) and intrauterine growth restriction (IUGR), their pathogenesis is based on the dysregulation of proliferation, differentiation, and invasion of cytotrophoblast cells that occur in the developing placenta, decidual endometrium, and myometrial parts of the spiral arteries. To understand the similarities and differences in the molecular mechanisms of PE and IUGR, samples of the placental bed and placental tissue were analyzed using protein mass spectrometry and the deep sequencing of small RNAs, followed by validation of the data obtained by quantitative RT-PCR in real time. A comparison of the transcriptome and proteomic profiles in the samples made it possible to conclude that the main changes in the molecular profile in IUGR occur in the placental bed, in contrast to PE, in which the majority of molecular changes occurs in the placenta. In placental bed samples, significant changes in the ratio of miRNA and its potential target gene expression levels were revealed, which were unique for IUGR (miR-30c-5p/VIM, miR-28-3p/VIM, miR-1-3p/ANXA2, miR-30c-5p/FBN1; miR-15b-5p/MYL6), unique for PE (miR-185-3p/FLNA), common for IUGR and PE (miR-30c-5p/YWHAZ and miR-654-3p/FGA), but all associated with abnormality in the hemostatic and vascular systems as well as with an inflammatory process at the fetal‒maternal interface.

Label-Free Quantitative Comparison of Cervical Mucus Peptides in Subjects With Endocervical Adenocarcinoma and Adenocarcinoma in Situ

Purpose:

To uncover potential diagnostic biomarkers for endocervical adenocarcinoma (EAC) and adenocarcinoma in situ (AIS).

Experimental design:

Quantitative label-free liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS/MS) peptidomics strategies were employed to profile 8 cervical mucus (CM) samples, including 3 EAC cases, 2 AIS cases and 3 normal controls (Ctrl).

Results:

Among the 3721 exclusive peptides identified, 12 (5 up-regulated and 7 down-regulated) endogenous peptides were significantly expressed in EAC compared to healthy controls (EAC/Ctrl); 10 (7 up-regulated and 3 down-regulated) endogenous peptides were significantly expressed in AIS compared to healthy controls (AIS/Ctrl); 11 (6 up-regulated and 5 down-regulated) endogenous peptides were significantly expressed in EAC compared to AIS (EAC/AIS) (absolute fold change ≥1.5, Benjamini-Hochberg adjusted p-value ≤0.05). Among these identifications, annexin A1 (ANXA1) was found to be down-regulated both in EAC and AIS, and its unique peptide (FIENEEQEYVQTVK) may be promising indicators for cervical glandular epithelial lesions.

Conclusion:

This is the first study to utilize CM peptidomics in cervical glandular malignancies, which may reveal the novel noninvasive biomarkers for EAC and AIS.

Combined Detection of ACTN4 and SCC-Ag is a Promising Serological Biomarker for Cervical Intraepithelial Neoplasia 3 or Worse: A Case-Control Study

Purpose

Cervical cancer (CC) is a common malignancy in women. Squamous cell carcinoma antigen (SCC-Ag) and cancer antigen (CA)-125 are widely used to help diagnose CC, but novel tumour markers with superior sensitivity and specificity are needed. α-Actinin 4(ACTN4) is overexpressed in CC, though its diagnostic value for CC is unclear. This study examined the diagnostic value of ACTN4 and SCC-Ag as biomarkers for cervical intraepithelial neoplasia (CIN) 3 or worse.

Methods

Women screened for CC at Fujian Medical University Union Hospital were recruited from 2017.1 to 2018.5. Cervical tissues and blood were collected at the same time. Patients pathologically diagnosed as CIN3+ or NILM/CIN1/CIN2 were classified into the case and control groups, respectively. ACTN4 mRNA and protein levels were detected through quantitative PCR and immunohistochemistry, respectively, and ACTN4 and SCC-Ag concentrations were analysed by ELISA. The sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), positive likelihood rate (PLR), negative likelihood rate (NLR), and Youden index (YI) of ACTN4 and SCC-Ag were evaluated. The optimum cut-off points for ACTN4 and SCC-Ag were determined by receiver operating characteristic (ROC) curve analysis, and accuracy was evaluated by the area under the ROC curve.

Results

In total, 105 patients were classified as CIN3+ cases and 106 as controls. The median ACTN4 levels in case and control tissues were 10.6 and 4.15, respectively. The ACTN4 and SCC-Ag concentrations were significantly higher in cases than controls (P_ACTN4=0.0007; P_SCC-Ag=0.0067). The sensitivity, specificity, PPV, NPV, PLR, NLR and YI of ACTN4 were 68.6%, 76.3%, 76.3%, 72.5%, 2.89, 0.41 and 44.9, respectively; SCC-Ag had a similar diagnostic value (P>0.05), and ACTN4 combined with SCC-Ag had a superior diagnostic value (75.6%, 87.5%, 88.6%, 73.7%, 6.05, 0.28, and 63.1, respectively).

Conclusion

Combined ACTN4 and SCC-Ag detection is a promising serological biomarker for patients with CIN3 or worse.

Progressive and Prognostic Performance of an Extracellular Matrix-Receptor Interaction Signature in Gastric Cancer

The role of an extracellular matrix- (ECM-) receptor interaction signature has not been fully clarified in gastric cancer. This study performed comprehensive analyses on the differentially expressed ECM-related genes, clinicopathologic features, and prognostic application in gastric cancer. The differentially expressed genes between tumorous and matched normal tissues in The Cancer Genome Atlas (TCGA) and validation cohorts were identified by a paired t-test. Consensus clusters were built to find the correlation between clinicopathologic features and subclusters. Then, the least absolute shrinkage and selection operator (lasso) method was used to construct a risk score model. Correlation analyses were made to reveal the relation between risk score-stratified subgroups and clinicopathologic features or significant signatures. In TCGA (26 pairs) and validation cohort (134 pairs), 25 ECM-related genes were significantly highly expressed and 11 genes were downexpressed in gastric cancer. ECM-based subclusters were slightly related to clinicopathologic features. We constructed a risk score model = 0.081∗log₂ (CD36) + 0.043∗log₂ (COL5A2) + 0.001∗log₂ (ITGB5) + 0.039∗log₂ (SDC2) + 0.135∗log₂ (SV2B) + 0.012∗log₂ (THBS1) + 0.068∗log₂ (VTN) + 0.023∗log₂ (VWF). The risk score model could well predict the outcome of patients with gastric cancer in both training (n = 351, HR: 1.807, 95% CI: 1.292-2.528, P = 0.00046) and validation (n = 300, HR: 1.866, 95% CI: 1.347-2.584, P = 0.00014) cohorts. Besides, risk score-based subgroups were associated with angiogenesis, cell adhesion molecules, complement and coagulation cascades, TGF-beta signaling, and mismatch repair-relevant signatures (P < 0.0001). By univariate (1.845, 95% CI: 1.382-2.462, P < 0.001) and multivariate (1.756, 95% CI: 1.284-2.402, P < 0.001) analyses, we regarded the risk score as an independent risk factor in gastric cancer. Our findings revealed that ECM compositions became accomplices in the tumorigenesis, progression, and poor survival of gastric cancer.

Is It Possible to Find Needles in a Haystack? Meta-Analysis of 1000+ MS/MS Files Provided by the Russian Proteomic Consortium for Mining Missing Proteins

Despite direct or indirect efforts of the proteomic community, the fraction of blind spots on the protein map is still significant. Almost 11% of human genes encode missing proteins; the existence of which proteins is still in doubt. Apparently, proteomics has reached a stage when more attention and curiosity need to be exerted in the identification of every novel protein in order to expand the unusual types of biomaterials and/or conditions. It seems that we have exhausted the current conventional approaches to the discovery of missing proteins and may need to investigate alternatives. Here, we present an approach to deciphering missing proteins based on the use of non-standard methodological solutions and encompassing diverse MS/MS data, obtained for rare types of biological samples by members of the Russian Proteomic community in the last five years. These data were re-analyzed in a uniform manner by three search engines, which are part of the SearchGUI package. The study resulted in the identification of two missing and five uncertain proteins detected with two peptides. Moreover, 149 proteins were detected with a single proteotypic peptide. Finally, we analyzed the gene expression levels to suggest feasible targets for further validation of missing and uncertain protein observations, which will fully meet the requirements of the international consortium. The MS data are available on the ProteomeXchange platform (PXD014300).

An integrated approach for mining precise RNA-based cervical cancer staging biomarkers

Since international federation of gynecology and obstetrics (FIGO) staging is mainly based on clinical assessment, an integrated approach for mining RNA based biomarkers for understanding the molecular deregulation of signaling pathways and RNAs in cervical cancer was proposed in this study. Publicly available data were mined for identifying significant RNAs after patient staging. Significant miRNA families were identified from mRNA-miRNA and lncRNA-miRNA interaction network analyses followed by stage specific mRNA-miRNA-lncRNA association network generation. Integrated bioinformatic analyses of selected mRNAs and lncRNAs were performed. Results suggest that HBA1, HBA2, HBB, SLC2A1, CXCL10 (stage I), PKIA (stage III) and S100A7 (stage IV) were important. miRNA family enrichment of interacting miRNA partners of selected RNAs indicated the enrichment of let-7 family. Assembly of collagen fibrils and other multimeric structures_Homosapiens_R-HSA-2022090 in pathway analysis and progesterone_CTD_00006624 in DSigDB analysis were the most significant and SLC2A1, hsa-miR-188-3p, hsa-miR-378a-3p and hsa-miR-150-5p were selected as survival markers.