Cancer Biomarkers - Science topic

thank you for answring my quesion dear Dr Erum Zafar

Dear Dr Mohammed,

I also suggest you to read these recent articles:

Best regards,

Pr Hambaba

Hi Anila...

Just to make more noise here... I routinely used this very cool webserver called sRNAtoolbox that will allow you also to analyze isomiRs together with many other small species. It's very cool, and specially designed for lazy people like me. It starts from raw sequencing data.

Take a look at:

The whole story in the NAR paper:

Be free to get in touch if you need help about.

Best. Paco

Please have a look at the following RG link.

X-ray people might be impacted more than NMR and cryo-EM people by AF2. It may replace all biophysical techniques for structural determination someday, IMHO, they advertise much better than academic groups for the things they've achieved and still a long way to go (like when Rosetta first introduced). Not to mention the missing pieces like non-natural amino acids, binding partners, dynamics, different circumstances in the cell, more or less scientists would like to validate the prediction experimentally. However, it is hard to argue with its valuable inputs and insights before wet bench works that cost a lot.

Nikita Demchenko you are welcome. Questions on RG is somewhat active. Glad to be of help. And yes 2.4ng/ml is specific to IgE. I figured you might be able to trace the timeline of using this IS unit system for CA-125, so now we know it is as old as 1984. I guess you can determine the protein concentration of your standards CA-125 (if you need this for ELISA unit conversion) by the Bradford or BCA assay and then extrapolate your sample's ng/ul conc against the standards' calculated concentrations. Hope this helps.

" Vimentin is a cytoskeleton intermediate filament protein present in cells of mesenchymal origin; this includes leukocytes, endothelial cells, and smooth muscle cells."

Diagnosis of most of the malignancies depends on the tissue diagnosis very high alpha-fetoprotein (AFP) in a cirrhotic patient or very high prostate specific antigen in a patient with enlarged prostate.

Diagnosis of most of the malignancies depends on the tissue diagnosis very high alpha-fetoprotein (AFP) in a cirrhotic patient or very high prostate specific antigen in a patient with enlarged prostate.

The role of cancer biomarkers e.g. CA 19-9 is if it is raised in a patient with a confirmed pancreatic malignancy by tissue diagnosis, is to serve as a baseline to follow up the patient after surgery or chemotherapy. Further rise or fall in the CA 19-9 will respectively indicate recurrence or disease free period.

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In addition, exosomes (from the secretome) could be subjected to mass spectrometry analysis to determine the presence or absence of potential biomarkers in the exosomal fraction. However, it must be stated that the integrity of the exosomes must be assessed either through the use of transmission electron microscopy (TEM) or by confirming the absence of cellular contaminations such as mitochodrion, ER, Golgi bodies etc.

Hi Adity Pore

A mesenchymal stem cells (MSCs) is one of the types of stem cells. It is mainly tissue-specific which means it has been isolated from different tissues mainly adult tissues. CD44 is one of the most prominent positive markers for MSCs while others are CD70, CD105, CD90, while negative markers are CD34, HLA-DR. However, the same CD44 is also considered as markers for breast cancer stem cells also.

The difference in markers of stem cells is because of their origin or site of isolation. For example, embryonic stem cells, Induced pluripotent stem cells, etc have different promising markers so those markers are being used for identification.

Now, Vimentin is an EMT marker that describes process within the cells, not cell types while CD surface markers are for cell-type identification markers here more specifically for stem cell identifications.

Yes, vimentin expression also has been analyzed in MSCs but it mostly to understand its characteristics that are fibroblastic nature which determines the EMT process let say cells migration ability which any cell will gain after they leave epithelium and start moving like mesenchymal cells. Vimentin use is not only for MSCs, it can be looked into any cell type, very common in cancer cells study purpose.

The whole concept is moving around the cell identification, characteristics, and processes carried out by any cells. Now, there are specific markers also there as well as overlapping markers are also there. This is because of origin and lineage memory. Please find a few attachments.

https://www.unmc.edu/stemcells/educational-resources/types.html

https://stemcells.nih.gov/info/2001report/appendixE.htm

I hope it will help you. If I went wrong please do let me know.

Regards

Saurabh

H820

MET amplification occurs with or without T790M mutations in EGFR mutant lung tumors with acquired resistance to gefitinib or erlotinib

Gamal Abdul Hamid Luis Rodrigo Wolfgang Doerr , check this out:

Alessandro Magrì et al. High-dose vitamin C enhances cancer immunotherapy, Science Translational Medicine (2020)

Hi

LGR5 is the best biomarker for detection of cancer stem cells in colorectal patients .

u can browse our my profile and see our paper about that

Regards

Yes, there are hundrds of advanced tools for Cancer Biomarker Discovery and Validation in different organ cancers. Nearly all cancers have their own specific markers.

just make search in pubmed or google for review articles regading any cancer.. for example in breast cancer just write in the search..

Prognostic and predictor markers in breast carcinoma review article.

you may use them for the reseach only, but they are both clinically insignificant. even in case of Ca. prostate, there is a lot of controversy about them, as well in BPH.

these two web address answers your questions

Just a small clarification.

The absolute numerical value of the net charge at pH 7 is important because it tells us what kind of protein we are dealing with. If the net charge is close to zero, we have a good chance that the protein is globular. If the net charge is different from zero for at least 2 units we must suspect that we are in the presence of a polyelectrolyte (polycation or polyanion). The greater the numerical difference, the more reliable the suspect is.

In this case we have a good chance that our protein is an IDP (Intrinsically Disordered Protein) or has large disordered segments (IDR). In both cases the protein behaves completely opposite to globular proteins (enough rigid with only very few conformers) because an IDP is extremely flexible and in physiological conditions behaves like a set of numerous different conformers. This population of conformers has the ability to interact with many (even hundreds) of different molecular partners depending on the chemical-physical conditions of the microenvironment. In this case the normal biophysical methods are not useful for the study of the protein. So knowing the net charge (and a sequence analysis) is important for quickly understanding what we have for our hands (see also Pappu's papers).

Hi Chistophe, you would have to 1. isolate DNA from each cell line, 2. PCR to amplify the region of interest, and 3. send sample for sequencing. You will have to make different sets of primers for each gene (total 10 primers, accounting for forward and reverse primers). If you need help with making specific primers, you can PM me, but there are lots of materials out there (Tm~60, ~20 bp, ~50% GC, 5'-heavy GC--test the primer on primer3plus prior to purchasing). Some tips in your case, make sure to design primers on the same exon and use a high fidelity polymerase, like phusion. The total cost varies, but a very conservative estimate would be ~$5 primer and ~$5 per sequence, so

2 cell lines *(5 to 10) sequencing primers + creating 10 primers = 100-150. Plus, you would have enough primer to last you a looong time in case you want to sequence other cell lines in the future.

Dear Shawana

You may find this article useful

Talanta. 2011 Oct 30;86:377-83. doi: 10.1016/j.talanta.2011.09.031. Epub 2011 Sep 22. Surface plasmon resonance based immunosensor for the detection of the cancer biomarker carcinoembryonic antigen.

Altintas Z1, Uludag Y, Gurbuz Y, Tothill IE.

Good luck

Sivakumaran

Hi Victor!

Although it is difficult to have a consensus internal reference control for cell-free RNA in blood, MIR30A5P and MIR99A5P can be considered as they are consistently expressed more or less stably.

I believe that single DNA-analysis in liquid biopsy would realize the precision medicine in cancer treatment because we can understand the heterogeneity of the tumor population and the dynamic tumor evolution!!

Liquid biopsy detection is promising method to detect cancer at early stage. Following the progresses of developing the sensitive methods to detect the cancer-related DNA or proteins in the blood, early detection for cancer becomes realistic.

good evening zahra, i am not sure! , i am looking forward to know those bio-markers and their levels in saliva

    Dear Shawana,

    You write:

     But for sensing, is it really necessary to conduct dynamic measurement (Resonance wavelength/angle shift vs. time)? For example, I can simply measure the shift in resonance by looking at the response curve (Reflectance vs. wavelength for example). 

    In short, the answer is yes. Obviously the resonance by itself is a dynamic process. In fact, the major advantage of kinetic analysis using Surface Plasmon Resonance for

biosensors is the option of determining separately distinct association and dissociation rate constants exceeding the classical steady-state analysis of biomolecules, 

@Tomas Koltai  and @Fatma Abdel Wahab 

The upcoming trend liquid biopsy is all about circulating tumor cells in the blood sample. How reliable will it be in predicting cancer like Breast Cancer???

Thank you Dr. Islam, ICGC was also great help for me.

Appreciate it.

Try xena.ucsc. You will fall in love with it.

Hi Manoj,

Welcome to Research Gate!!!!

As far as I know, there are no somatic gene panels reported till date for breast cancer.

The best way you can follow is to collect frequent mutations in a population. You can explore databases like COSMIC, TCGA, ICGC, CCG for your analysis.

Also, see attached articles. Hope it helps

Feel free to share any doubts....

What is your Suggestion

 This is a stage IV by definition , if the  pleural effusion is symptomatic then drainage for symptomatic fast relieve is indicated , if not symptomatic then will start systemic therapy with any EGFR TKI ( erlotinib, gefitinib, and afatinib ) all have efficacy in EGFR-mutant lung cancer and are generally well tolerated.

The choice will depend on the availability , cost , toxicity profile , physician comfort with the chosen agent  , some reports indicates that  afatinib may yield the strongest disease outcomes but may also cause the most side effects. Some reports also indicates gefitinib may be the best tolerated agents.

Dear Martyna, you need to look on the literature devoted to DAMPs and alarmins. Here is the review, which is useful to start search. https://www.ncbi.nlm.nih.gov/pubmed/27101817

Thank you fro your suggestions!

Currently, I would say, the closest to clinical practice technology of identifying rare cancer mutant alleles is a technology based on sequencing of cell-free DNA (cfDNA)  utilizing unique barcodes to each DNA molecule (actually each DNA fragment as cfDNA is fragmented. The problem with CTC is that, although it contains the whole genome DNA, it represents only a part of cancer tissue and this is a problem as cancer is often highly heterogeneous. 

CTCs were first described in 1869 in patients with cancer by Asworth . They are epithelial tumor cells already found in the peripheral blood of patients with cancer at an early stage by Cristofanilli et al. 2005. It was long assumed that its presence in the blood meant progression of neoplastic disease and could be directly related to the appearance of tumor metastases. But its true biological meaning could not be established by its small number and by not having at that time with techniques that allowed its isolation and identification

recent papers have identified Matriptase as being critically involved in breast cancer progression and represents a potential therapeutic target in breast cancer by regulating c-Met mediated proliferation and invasion in inflammatory ovarian cancer as well. early studies had also identified it's rule in colon and prostate tumors invasion and metastasis.

Thanks Prasanth

Hello Heba

The high confidence miRs are those with high probability of expression level according to readings of sequencement to identify them. This readings are notated in miRBase. 

 These miRs are useful to screaning the miRs with some functional effect according to its high expression (database).

Best regards

Thank you Dr. Aline C Planello

Thanks-Waqas. It is very helpful. Best wishes.

Did you manage to make this work? I've tried several times and I encountered some obstacles. First, yields from the initial FASP preparation is surprisingly low, according to Zielinska et al you need approx 100 µg, I never got close to that. Also, the lectins seem to behave weird... when I dissolve them, they seem ok, but after mixing with the peptides they seem to precipitate. I don't know if they are worth something after that. And lastly, 3 hours seem to me too short incubation time for PNGase F to work. I've tested it and after 3 hours, only a fraction of glycoproteins were shifted on SDS-PAGE, whereas ofter over-night incubation, the enzyme deglycosylated a major part.

Dear Gnanasekaran

You can use from FOBT for cancer diagnosis in colorectal cancer

Best wishes

Mohammad Amin

I depends. There are groups running mRNA analysis from "whole blood", but fyi you usually use the plasma, unless we're taking about whole blood cells.  However there are many things to consider and I would recommend you read up on this topic. For example mRNA rapidly degrades so age, storage and preparation of samples is paramount. Also, the type of mRNA (ie. sequence length, pcr system, etc.) will effect the accuracy and stability of the technique you plan to use. To your last question, yes you will often but not always get different profiles from tumor and plasma. But again this depends on a number of assay factors. This discordance can be good or bad, depending on your final results. Again, there are many groups publishing this type of analysis and I recommend you read up before you design your experiments.

Mr. Arvind,

I already enquiry to those labs as they don't use Imaging Flow Cytometry.

In addition, some links. According to this study,

oxidative stress kills BRCA1-deficient cells

in normal tissue. But in tissues with estrogen,

cells are repaired with Nrf2.

Other:

Regards,

Joachim

Hello Agbas,

In principle, yes, you can try this way. But you need to determine the dilutional recovery of these pooled plasma (undilution, 2x, 4x, 8x, etc) in the first place. For instance, you see nice recovery after 2xdilution, then 2xdiluted pooled plasam can be used as the first standard point of the curve. You may assign it as 1000ng/ml, 1000ug/ml or whatever you like to quantitate your target protein.

However, I would recommend you synthesize the peptide recognized by the antibody in your assay if you by chance know the epitope. Otherwise, just try the way abovementioned.

I hope it helps.

Roy

Dear DP,

There are no particularly defined markers for determining breast cancer stage at present. You can find details here:

Dear Jacques Gilloteaux,

I have checked the literature through pubmed. But, some are still now confusing.suppose, biomaker CD44+ and CD 90+ (double positive) cells are available on cancer cells as well as liver cancer stem cells. But, till now, I didn't get any articles about the presence of those marker on health liver cells  as well as liver stem cells. I badly need those biomaker which are only present on both cancer cells  and cancer stem cells for targeted therapy not health cells or health stem cells.

Thank you.

Hi Farideh

You can use cel-miR-39 or whatever other spike-in control to check either the extraction of your RNA (by adding the spike in before) or the efficiency of the cDNA synthesis, by adding the spike-in after RNA extraction. I would recommend to use two different synthetic spike-in molecules if you wish to check for both quantification steps.

Best luck.

Paco

Hello,

I would recommend a free antibody database available at labome.com. For antibodies to Snail for IHC you can check the following link: https://www.labome.com/review/gene/human/SNAI1-antibody.html. Santa Cruz Biotechnology has rabbit polyclonal (H-130) sc-28199 ab suitable for IHC on human samples (Liu et al., Mol Oncol. 2015). In addition, Invitrogen has  PAS-11923 ab for IHC at 1:200 (Fang et al., Hepatology 2015). Cell Signaling Technology offers C15D3 ab for IHC on human samples at 1:100 (Luo et al., Virchows Arch. 2014).

We may find circulating cancer cells by analyzing genetic cancer markers.  One of my friends has started a company, Genomictree, with this concept. Please visit following site.  http://genomictree.com/en/technology-2/dna-methylation/

Overall, PSA is the most widely used.

Yes. There are several things one would need to consider very carefully before claiming VAV3 as a good diagnostic marker in CRC or designing the diagnostic test for CRC using the method you proposed. Here are a few that come to mind.

1. There seems to be only one paper that links VAV3 over-expression to CRC (http://www.nature.com/articles/srep09360).

2. This paper linked VAV3 immunohistochemical positivity in CRC vs normal colon using FFPE tissue, finding that VAV3 protein over-expression is an independent prognostic marker in CRC. I do not believe that they showed that the level RNA expression of VAV3 in CRC is correlated to over-expression of VAV3 protein. There are other means by which protein levels can be regulated. That should be tested first before one extrapolates correlation to RNA.

3. Don't think they looked at VAV3 expression in polyps. Is VAV3 over-expression in polyps correlated to development of CRC later on? At what level of over-expression (RNA and protein) is there an increased risk to develop CRC?

4. 11% of tumour samples in one of their patient cohorts were completely negative for VAV3 protein expression.

5. They split patients into two groups, low and high VAV3 protein expression levels and did Kaplan-Meier survival plots. High VAV3 patients did worse than low VAV3 patients. Can one detect a statistically significant difference in VAV3 RNA expression in CRC to stratify patients into these two groups? Will VAV3 RNA levels in polyps be significantly different enough from normal tissue  to make a claim of the likelihood of CRC or possibility of CRC down the line. What are the thresholds?

6. Sample preparation/storage....fresh biopsy vs FFPE.

Inorganic azides such as sodium azide are very strong nucleophiles, probably one of the strongest known and they will interfere with reaction by consuming some amount of NHS ester. This AB is offered in 100 ug amount =, which is ca. 0.67x10^-9 mole (FW ca. 150,000), and I presume in is in 100 uL (10^-4L). If I correct concentration of AB is around 0.67x10^-5 M or 0.67x10^-2 mM. It is supplied in 15 mM sodium azide, which is about 4000 fold excess. Even if 100 fold excess of labeling reagent is used, there is still about 40 azide molecules (ions) per 1 molecule of NHS ester.

I did several NHS labeling reactions in the presence of sodium azide, at best I call it inconsistent. It is very simple and quick to desalt small amounts of proteins with Zeba columns, it takes 5 min an will remove up to 95% storage buffer.

Also, there is another supplier of PC Biotin-NHS Ester https://clickchemistrytools.com/product/pc-biotin-nhs-ester/ You can also find an easy to use protein labeling on the same page.

In really, it is not a pustule because do not have signal of purulent secretion. Make a biopsy may help you with the diagnosis. Do you think that it could be a metastasis? Solid and fixed mass in cancer animal model seems to me a tumor.

Dear Wael, 

check with the authors to these papers here on RG: 

I will suggest you to try with RUN48 as endogenous control for RT-qPCR. We worked with this and is fine with human samples. You will get the universal primer from kit that you will use for cDNA conversion.

 Hi.

 You can sort fibroblast  by EpCAM (-)  FSP1 (+) cells. If you want to be sure that you don’t have any contamination with leucocytes then  exclude  CD45+ cells.

Best.

 which sequence did you order?

A lot of good points raised but most exhibit a proclivity to the primary tumor "doing things" that subsequently result in metastases - we should also consider the roles played by the pre-cancerous niche and how the microenvironment where the  metastasis occurs facilitates the "seeding" of the cancer- so how would one weight the role of a traveling cancer cell against the role of the environment where the metastases ends up occurring?

In case of less comlex solutions, sometimes you can get a supercooled state,.  In this case, if you just lightly shake the tube it will freeze right in your hand !  In case of FBS, I would add that you should make sure your freezer is at -20C to get it to freeze.  The door of these freezers is much warmer than the inside, especially if you keep opening the freezer often, and even PBS solutions sometimes do not freeze.  In the latter case, then you know it is not keeping temperature.

Maybe it is to late but I think you can look at the following paper Microarray-  and metabolomics study:

PMID: 20059769 Microarray study

PMID: 24721970 Metabolomics Study

I hope it is useful...

Given that multiple myeloma arises due to the monoclonal expansion of abnormal plasma cells, which leads to the production of monoclonal antibody characterized by Bence-Jones protein, IgG, IgA, IgM, which is produced in a mutually exclusive manner depending on a clinical case. That is why the typical concept of cancer stem cells in the heterogeneous tumor cell society is difficult to find in multiple myeloma. 

1) The limit of detection (LOD) based on calibration curve slope is determined as 3SD[y/x] / slope. The result is already in concentration units (no need for conversion). SD[y/x] is not the standard deviation of responses, but the standard error of the regression, which is calculated from regression residuals (actual response - fitted response). 

2) Alternatively, LOD can be determined from average and standard deviation of blank measurements as follows: y=average blank+3SD[blank]; y is than converted to LOD in concentration units using the calibration curve. SD[blank] is the standard deviation of blank measurements.

try to extract spectra from different regions (intensity related differences) e.g some from blue or orange regions and post here. We can check for DNA damage, protein content etc...then we can take a call.. 

Hi. You can search for your protein network (TGF-beta) with CYTOSCAPE. You could copy paste the list of your interacting proteins and then use GO ontology to look for the genes implicated in EMT process. Hope this may help you.

Proper regulation of white and brown adipogenic differentiation is important for maintaining an organism's metabolic profile in a homeostatic state. The recent observations showing that the p53 tumor suppressor plays a role in metabolism raise the question of whether it is involved in the regulation of white and brown adipocyte differentiation. By using several in vitro models, representing various stages of white adipocyte differentiation, we found that p53 exerts a suppressive effect on white adipocyte differentiation in both mouse and human cells. Moreover, our in vivo analysis indicated that p53 is implicated in protection against diet-induced obesity. In striking contrast, our data shows that p53 exerts a positive regulatory effect on brown adipocyte differentiation. Abrogation of p53 function in skeletal muscle committed cells reduced their capacity to differentiate into brown adipocytes and histological analysis of brown adipose tissue revealed an impaired morphology in both embryonic and adult p53-null mice. Thus, depending on the specific adipogenic differentiation program, p53 may exert a positive or a negative effect. This cell type dependent regulation reflects an additional modality of p53 in maintaining a homeostatic state, not only in the cell, but also in the organism at large.

The more doublings of your population, the higher the probability that mutants bearing deletions will arise and overtake the culture. Most likely you already have mutants in the 5 mL culture, but at proportions low enough to pass below the limit of detection of your assay (restriction digestion + gel electrophoresis).

Have you tried E. coli strains designed to propagate repetitive sequences, such as SURE or STBL3?

The epithelial-mesenchymal transition (EMT) is a process in which epithelial cells lose their cell polarity and cell-cell adhesion, and gain migratory and invasive properties to become mesenchymal stem cells. E-cadherin is a protein that in humans is encoded by the CDH1 gene and down regulated during early stages of carcinogenics.

Good Luck

Dear Narayanaswamy,

maybe you can also find interesting "aptamers" at SOMAlogic (http://www.somalogic.com/). They are selling small binders, which are a hybride between DNA and Protein.

Regards Volker

Poštovana Danijela, 

Interesantne podatke možete naći na linku:

First do IHC, if the link is confirmed, then carry on with ELISA or WB

sorry no

Use link below to find splice variants of any human or mice gene. I quick search revealed 14 variants of human BRCA1 gene.

link: http://projects.insilico.us/SpliceMiner/Gene.jsp

Dear JK,

The attached file is a recent published review that covers the answer to your question.

Context.—Radiation is a key arm in the multidisciplinary treatment of patients with head and neck squamous cell carcinoma. During the past 2 decades, significant

changes in the way radiation therapy is planned and delivered have improved efficacy and decreased toxicity. Refined approaches in the application of radiation and chemoradiation have led to organ-sparing treatment regimens for laryngeal and pharyngeal cancers and have improved local and regional control rates in the postoperative, adjuvant setting. The molecular and genetic determinants of tumor cell response to radiation have been studied, and several potential biomarkers are

emerging that could further improve application and efficacy of radiation treatment in head and neck squamous cell carcinoma.

Objective.—To discuss the current understanding of potential biomarkers related to radiation response in head and neck squamous cell carcinoma.

Data Sources.—Existing published literature. 

Conclusions.—Several potential biomarkers are actively being studied as predictors and targets to improve the use and efficacy of radiation therapy to treat head and neck squamous cell carcinoma. Several promising candidates have been defined, and new markers are on the horizon.

This review has highlighted several biomarkers that are actively being studied as predictors and targets to improve the use and efficacy of radiation therapy to treat HNSCC. Several promising candidates have been defined, and new markers are surely on the horizon. Biomarkers that lead to significant improvements in patient outcome will require rigorous validation and prospective testing.

Hoping this will be helpful,

Rafik

you can run protein antibody array and compare the expression in normal versus malignant tissue

“NF-κB and STAT3 – key players in liver inflammation and cancer” maybe this review could have some help for you.