Cancer Biomarkers - Science topic
A biological molecule found in blood, other body fluids, or tissues that is a sign of a normal or abnormal process, or of a condition or disease. A biomarker may be used to see how well the body responds to a treatment for a disease or condition. Also called molecular marker and signature molecule. A cancer biomarker pertains to any biomarker that fits the aforementioned definition but only for cancer, and no other disease.
Questions related to Cancer Biomarkers
We want to know if one protein can be used as a breast cancer biomarker or not. So we'll have to compare normal and patients, and our question is whether we can get samples from patients who received chemotherapy before?
there are various bioinformatics tools that show the patients' mortality rate related to gene expression such as prognoscan! if you know other bioinformatics platforms or approaches please let me know!!!
Any suggestions on preferred online tools for analysing small RNA seq data (isomiRs differential expressions) for those researchers who don't have any bioinformatics background.
SV40 is not considered an oncogenic virus in this review:
Article Oncogenic viruses and cancer
Why is SV40 not considered an oncogenic virus when it produces the large T antigen, which is used to immortalize mammalian cell lines?
Additionally, SV40 proteins have been found in human tumors.
Could this lack of coverage possibly have something to do with the fact that the polio vaccine introduced SV40 into the human population in the late 1950’s? How many people are actually positive for SV40 proteins? How many of these people develop cancer? Why are SV40 proteins not tested for regularly, given that they are an indicator of cancer?
AF2 may most strongly impact experimental determination of protein structure by multiple methods with possible benefits and negative impacts over time.
Some areas may need to quickly pivot or become obsolescent, whereas other may thrive.
Structures of large macromolecular machines should be enabled by having accurate computational structures for subunits and components.
The already great value of sequence data (which is doubling every 8 months) is likely to become far greater by being more directly connected to spatial information.
Overall the pace of biology and biophysical advances can be expected in increase by the ability to better harness the flood of sequence data.
What do you think?
My current project involves measurements of CA-125 and some of the apparatus we use gives an output in pg/ml whereas the standard measurement unit of concentration in serum for this antigen is u/ml.
u/ml is a unit usually used for measurement of enzymes and for concentration of immunoglobulins. CA-125 is neither of those. It has no enzymatic activity one can measure.
So, how do I convert between the two units of concentration if I want to compare?
I am staining patient blood sample slides for identifying CTCs and I use the epithelial marker pan cytokeratin and mesenchymal marker Vimentin. I stain WBCs for CD45 marker. And I have seen that almost a big chunk (~60%) of my WBCs stain positive for vimentin . I am using the technique of immunofluorescence. Can someone please tell me the reason for this?
CA19-9 is a commonly performed tumour marker in pancreatico -biliary malignancy,but the levels keeps varying ? depending on the severity of obstruction causing cholangitis.In these circumstances if the levels are high does it mean it is a disseminated malignancy or it is probably due to cholangitis !
When you purify extracellular vesicles, such as exosomes, what are your downstream applications/analyses? I'm especially interested in understanding what your next steps are if you're doing biomarker discover or diagnostic research.
Thanks in advance for your input!
For example CD44 is a stem cell marker, whereas Vimentin is an EMT marker. Mesenchymal cells are called MSCs (Mesenchymal Stem Cells), then why are there different markers for stem cells and mesenchymal cells?
Hello. i am searching for well known (used in clinic) molecular markers with their criteria in breast cancer. i found many signature sets like, PAM50, MammaPrint. i wonder if there is reference of in details information for all these markers
"In conclusion, high-dose intravenous ascorbate represents a promising and inexpensive anticancer therapeutic option that should be further explored in clinical trials. Given its low toxicity and low financial cost, ascorbate could become an important weapon in our arsenal against cancer, either acting as a single agent with predictive biomarkers or used in combination as an adjuvant therapy."
Targeting cancer vulnerabilities with high-dose vitamin C
Bryan Ngo, Justin M. Van Riper, Lewis C. Cantley & Jihye Yun
Nature Reviews Cancer volume 19, pages 271–282 (April 2019)
Invitation: Start a clinical trial.
There are currently 15 clinical trials. See details of those trials here: https://www.nature.com/articles/s41568-019-0135-7/tables/1
The event of death by metastasis or recurrence is very common, many researchers have linked the tendency of some tumors to re-appear to the presence of occult or dormant cancer cells that may have a phenotype that allows them to remain "hidden" from the immune response. However, the understanding of these cells and the mechanisms that they use to achieve evasion remain mostly unknown. It is critical to understand these cells better and to be able to detect their presence for they are of great therapeutic importance.
tools or servers for determining important biomarkers in many cancer, for example, glioblastoma multiforme (GBM) or breast cancer and others??
I'm conducting a research on the Chemoprevention of testosterone induced BPH on Rats using some food plants.
is there any publish research show the salivary biomarkers concentration for breast cancer?
iam trying to design a salivary biosensor for early detection of breast cancer. recommend me some articles please
I'd like to characterize 2 mouse cell lines in terms of mutations and would like to know if you had good primers and protocol (or any other way to test it) to test the following genes:
Kras (codon 12-13-61), Braf (V600E), Pten, Egfr, Pi3kca (exon 20).
Thank you in advance for your responses.
Can someone please suggest me some research articles for the detection of lung and ovarian cancer using Surface plasmon resonance (SPR)? I found lot of research papers on prostate, breast and colorectal cancer detection, but found only one article for lung cancer (V. Sahu et. al. 2016) and one on ovarian cancer (J. Yuan et. al. 2012) detection using SPR.
I am only interested in SPR detection method.
Thanks in advance!
We are trying to analyse differential expression of cell free mRNA (which is totally free on the blood) on blood samples of breast cancer patients. I need articles to use as references. Thanks!
The potential applications of single cell genomics include biomarker discovery, clinical trials, therapy selection, and disease monitoring.
What is the importance of single-cell biology to understand how clonal diversity in cancer impacts response, resistance, and relapse?
How single-cell DNA analysis overcomes the limitations of bulk sequencing to understand clonal architecture and mutation co-occurrence which impacts hematological malignancies?
Most cancers are detected when they cause symptoms that lead to medical evaluation. Unfortunately, in too many cases this results in diagnosis of cancers that are locally invasive or already metastatic and hence no longer curable with surgical resection or radiation treatment. Medical therapies, which might be curative in the setting of minimal tumor burden, typically provide more limited benefit in more advanced cancers, given the emergence of drug resistance.
i went to know the biomarkers level of breast cancer in saliva,
if any one worked in this area ?
I am using surface plasmon resonance for cancer biomarker detection. I know the dynamic measurement helps in understanding the association and dissociation of biomolecules to the sensor surface. But how does it help in overall sensing/detection?
I want to detect the somatic mutations for breast cancer disease. Can anyone tell me about the major differences in detecting somatic mutations from blood sample and tissue samples
I want to see mutations and allele frequencies in oncogenes in a prostate cancer, but I need a tool that could provide information in free access accounts. I tried oncomine but it has some restrictions which is why I want to look for another one.
I need to compare a gene's expression between tumor site and matched normal tissue from TCGA database. I've tried using Firehose to search differential expression of the gene among different types of cancers. The problem is that the amount of tumor samples is not equal to the amount of normal samples. But I need to compare matched tumors and normal tissues. Is there any tools to do that?
Is there any somatic mutation gene panel for detecting breast cancer?
I already know there are Germline mutation gene panel for Breast Cancer
I am new to the field of immunology. I am trying to understand the different sources of cancer neoantigens and they can be utilized for immunotherapies. In one of the books, I read that 'tumor-specific neoantigens can be treated as self if they do not cause inflammation'. I guess that's why cancer vaccines etc. are administered with adjuvants. However, what usually causes inflammation in the context of cancer so that the neoantigens are recognized as foreign? Is it due to the rapid growth of the tumor and destruction of neighboring tissue or cancer cell death?
I would appreciate any feedback.
To determine microsatellite instability in a cancer patient sample, it is necessary to compare the parallel samples i.e. tumor tissue and peripheral blood. How the microsatellite instability or stability is determined in a cell line?
Can anyone provide me some trends on circulating disease markers (exosomes or CTCs) as below?
1. Current challenges in characterization (selectivity)
2. Leading technologies (early diagnosis / sensing)
your kind responses will be very appreciated !
I am working with CTCs separation and analysis. I have not found any paper on CTCs subclasses classification and the detection method using molecular tools. Where can I get knowledge about CTC subclasses distribution?
Protein extraction kit for dogs.
Molecular characterization of proteins (Proteomics)
Required to have some papers related to environmental impact over cancerous cell singling.Very simple and easy to understand for my internship work.
I try to detect the gene methylation in cervical cancer patients and abnormal cytology comparing with normal cytology of cervical scarping by Methylation specific PCR method. In addition, some normal cervix sample showed the methylation band. Is it possible to detect in normal sample?
Recently genomics have made unprecedented inroads into cancer diagnostics. With the cost of DNA/RNA sequencing coming down significantly in the last few years and the next-generation-sequencing (NGS) bringing speed, accuracy & reliability, we are certainly in the SCIENTIFIC BREAKTHROUGH ERA! Scientists are developing "DNA/RNA CHIPS" or some Biotechs are already in beta-testing for diagnostics/prognostics/drug discovery kits, which intend to reduce timelines and will be less resource-intensive. These kits are now on the move from LAB-TO-CLINIC-TO-OR (Operating room)......We are witnessing a REVOLUTION IN PERSONALIZED MEDICINE, where ultimate beneficiary will be THE PATIENT! Obviously, in the right scenario, TARGETED THERAPY for the SPECIFIC STAGE(S) OF TUMOR DEVELOPMENT, instead of relying primarily on PHENOTYPIC PATHOLOGY? In addition, portable instruments reading RNA/DNA CHIPS will provide accurate diagnostics at POINT-OF-CARE and hopefully, will make the life of pathologist/oncologist/physician/scientist less stressful......Your thoughts-please.
I am interested in lentil lectin sepharose glycoenrichment methods protocol.
I plan to study mRNA expression of some biomarkers e.g. p53, hTERT, Wnt7A by quantitative PCR from ovarian cancer patients. Can I do the analysis using whole blood samples from patients instead of tumor tissue? Will I get the same expression profile for both whole blood samples as well as tumor tissues?
BRCA 1 and 2 are involved in the HR DNA repair pathway and they have an ubiquitous distribution in the whole body. I just wonder myself why is there a higher risk of breast or/and ovarian cancer when BRCA1 or/and 2 are mutated compared to other type of cancers ? If the HR DNA repair pathway is impaired, I would like tothink there is the same risk to develop a new cancer in all type of cells, rationally. So, are there other mechanisms known which could rescue cells in other type of cells ? Anything else ?
Thank you for your help.
I am working on a development of blood-based biomarker protein for AD and ALS; however, protein candidate is not readily available in purified form. Therefore, I have the problem of not having calibration curve to quantitate this protein. I was thinking that if I collect , say 50 plasma samples and I know that the bio-marker protein is elevated. Pooled these plasma and construct a calibration curve based on their total protein content. Now, I have a kind of dose/response curve. I am asking my fellow researchers that is this way a legit. I know it is not ideal, but i stacked with the absence of the purified form of this protein. We have attempted, but it is quite unstable. Any recommendation, thoughts, tips are welcome.
In different grades of breast cancer cell line , what are the reference genes/proteins can be used?
Is there any biomarker on liver cancer cells which are not present on health cells? Many papers revealed that many biomarkers are abundantly expressed on cancer cell but they are also present on health cells. I am searching specific biomarkers which only represent cancer cells.
I am interested in looking at the expression of some EMT markers in human breast tumor samples. It's difficult to find good antibodies. Especially in the case of Snail (Snai1), most papers list the company that produced the antibody but not the catalog number. Often times there are several antibodies from one company. Looking to see if anybody tested and identified ones that work well for IHC on FFPE samples. Thank you!
Almost all of our cells are directly connected to the blood circulation.
Thousands of our cells die every hour and spill their contents into the circulation to be cleared by the liver and kidneys.
All blood samples will contain DNA from normal cells. If you have an infection, injury or inflammation you will have more DNA in your blood.
Based on this I don't understand the value of looking at cell free DNA from cancer patients as a potential diagnostic.
Some like to call it circulating tumor DNA (ctDNA), but can you really link any plasma DNA mutations to primary tumors or metastasis?
What is the most important and most used cancer markers (proteins) in human blood plasma that is in use today, and which do you think is going to be the most important cancer markers in blood plasma in the coming years for early detection of the most unfolded types of cancer?
If you know about some new research papers in this area, they are very welcome.
Take a sample from the suspected area, polyp, ulcer etc. Extract RNA from these cells. Convert to cDNA and do real time PCR to determine whether the oncogene VAV3 is over expressed? (VAV3 is highly linked to CRC).
I am looking forward to conjugate PSA antibodies (Monoclonal, Mouse, IgG1 - A67-B/E3 ) available at
with photo-cleavable biotin NHS ester available at (http://www.ambergen.com/technology/pc_linkers.asp).
The antibodies are coming in a solution having Sodium Azide.
Is it necessary to remove sodium azide from the solution or can it be used with it as well. Secondly, if it needs to be removed, what is the best and quickest way to remove it.
It would be great if anyone would share a protocol or a much simple approach for conjugation of PSA antibodies with the above mentioned photo-cleavable biotin.
During our experiments we noticed that nude mice orthotopically grafted with GBM, develop cutaneous pustules when treated with TMZ (schedule: 1 week on and 2 weeks off for 6 cycles). We couldn't identify any bacterial or viral infectious with standard tests. Moreover, these pustules affect the survival of mice.
Does anyone has already faced this phenomena using TMZ and is there any explanation?
Hi! I am new to RT-qPCR and I have the following question.
We are planning to measure some miRs in plasma in a longitudinal cohort. As far as I know, there aren't any generally accepted reference genes to use as endogenous controls for plasma.
We are thinking using absolute quantification with synthetic miR standards and report results as copies/ul of plasma.
If we use AQ, do we still need to normalise against eg. cel-miR-39, to account for variability in extraction? What would be the best method for normalisation in this case? Thank you in advance!
I am going to use bombesin as a ligand for detection of MCF-7 breast cancer cell lines and I am going to order bombesin peptide, but I do not know what is the best peptide sequence of bombesin for this research to detect MCF-7 breast cancer cell lines specifically.
Is metastasis something that every cancer cell can and will do at some point or are there genetic mutations or epigenetic changes are results in metastasis?
This was drawn for an ENOX2 test. The patient had mildly elevated Calcium, TP, Albumin, and ALT. All other labs were normal except a chronically high Lp(a).
Patient developed Shingles at about the same time.
Hello Every body,
I am working on detection of cancer biomarker and I get the calibration curve.
I calculate the detection limit by obtain the 3*std/slope. but the result doesnt make any sense !
I used range of concentration and the response is current. I got the std of the current values and multiply by 3 then I substitute the result in the calibration equation to get the concentration but I got value higher than my smallest value of concentration that used to generate the calibration curve .
Hello everyone, i have oral skin sample which is effected by a cancer. I have no idea about what kind of cancer is and what looks like a cancereous cell because i have no biological background. So any biophysicist or biologist would like to help me. In my last question i have attached its picture now i am attaching it 2nd time.
In my work am trying to construction EMT( Epithelial to mesenchymal transition) pathway induced by TGF-β but I am finding difficulties while construction i.e.,
whether pathway constructed for particular cancer is effective or in general
(because the TGF-β downstream signals are same i e SMAD and non-SMAD signal are same for all type of cancer)
Is there a particular feature or a direct connection that can explain why immunohistochemical expression of mutant protein p53 is increased in obese and diabetics (type 2 diabetic) patients at diagnosis of colorectal adenocarcinoma compared to non -obese diabetics versus non-diabetics obese/non obese?
Study included immunohistochemical analysis of 2 proteins Bcl2 and p53 (both monoexpression and coexpression) in 100 newly diagnosed colorectal adenocarcinoma specimens divided equal in 2 groups diabetics (type 2 diabetes mellitus already existing at diagnosis of colorectal cancer) and non-diabetics .The preliminary statistics results have not indicated a significant difference between the 2 groups, in terms of Bcl2, but indicates an increased expression of p53 only in the diabetic-obese group compared to non-diabetics obese or non-obese (statistically significant ) which theoretically indicates a contact point between obesity, cancer and diabetes. Interestingly moderately low degree of differentiation is associated with both diabetes and the presence of p53 positivity; G2-p53 associations is an intriguing part. Bcl2 expression was low and insignificant in both group.
I have cloned my 3.3Kb insert having repetitive sequence in yeast expression vector, by directional cloning in E.coli. Positive Clone of 8.7Kb was confirmed by restriction analysis. While the same positive E.coli transformants when grown in 100ml LB, the restriction pattern observed is different. But the the digestion pattern is as expected when it is isolated from 5ml culture. Could anyone please let me know why this discrepancy observed from 5ml to 100ml scale up.
I am planning to culture MCF10 cells with different carcinogens,can some suggest a marker which I can look for as a sign of early malignant transformation.
I want to design a study to assess whether an untested protein could be used as a biomarker for human pancreatic cancer. I intend to do immunohistochemistry of this protein in pancreatic tumour tissue and normal tissue. I am thinking of doing TMA and normal tissue microarray. Should I include any other assays like ELISA of body fluids and Western blotting for validating this protein?
These cell lines along with available xenografts and other factors along with other biomarkers ( if you have any it would be appreciated) will be used to build a preclinical model for high risk Wilms tumors. The development of assays specific to this model will result in the ability to do novel cell line and animal testing which could potentially lead to clinical trials with new compounds for children with these disease.
I know BRCA1 on ch17q21 have 29 transcript variants I found 7 of them on NCBI but, I couldn't find others.
Can anyone please help me find them?
Also I know BRCA1 has 24 exons, but where can I find their range on DNA?
I would appreciate any help.
I am looking at studying the connection between NF-kB and JAK/STAT3 in normal and cancer cells. I am pretty certain from my research that there is a connection with IL-6. What type of tests should I propose to test this and what would some expected results be?
I am part of a multidisciplinary research group at the University of Saskatchewan Canada, who are studying prostate cancer. I am wondering if there is well established research protocol to induce prostate carcinoma in dogs. We need dogs with prostate carcinoma to use for imaging studies.
Anybody who has a protocol or can help do this and would like to establish collaboration?