- Mehrdad Payandeh added an answer:What is the new tumor suppressor gene for prostate cancer?
For evaluation of tumor response and toxicity in prostate cancer cells.
If we want to check the cancer cells response to the adjuvant radiation therapy or combination of three or two modalities in prostate cancer, what biomarker could help us? What is the newer and recent androgen receptor?
Ki67 level and mitotic indexFollowing
- Xiaolong Zhang added an answer:What stemness genes can be used for cell classification using expression data?
I have sequenced tens of single cells of bladder cancer, and got the gene expression profile of each single cell. I am trying to speculate the cancer stem cells mixed in these cells using clustering method, which needs a priori list of "stemness genes". If there are some available common or specific stemness signatures can be used in this analysis? Many thanks.
Thank you Go J Yoshida and Shi Lei. Actually I have sorted the "cancer stem-like cells" as CD44+ by FACS, as well as CD44- cancer cells and normal epithelial cells. But CD44 is just a marker to enrich CSCs. So I need a more comprehensive gene list to infer the more likely CSCs in these sorted cells.Following
- Kulvinder kochar kaur added an answer:Cancer a mere matter of luck? Or is there something under-appreciated?
It has been all over in the news lately: The majority of cancer is obtained by bad luck, not by lifestyle or inheritance. See attached.
Really? The data appear solid and they make sense, but the conclusion seems a bit premature: the observations are based on established risk factors in the USA and I assume (let the experts please come forward!) that these risk factors are based on occurrence. This means we do not see all those cases where the patient's immune system adequately takes care of the anomaly.
How does occurrence of cancer relate to failure of the patient's immune system, and can we monitor this based on adequate biomarkers? How will the statistics and the conclusions change when this factor is included in the analysis?
thanks for the reference will read it and get backFollowing
- Ahmed Jarad added an answer:Can all malignant tumors (cancers) metastasize to other organs?Cancers metastasize via seeding through blood or lymphatic vessels.
not all cancer(malignant) metastasis like basal cell carcinoma is malignant but not metstasisFollowing
- Tahmina C Islam added an answer:Can cancer come from any type of cell or are there some cell types that never produce cancer?Some cells seem to produce cancers more frequently than others. There are > 200 distinct human cell types; do all of these produce cancers under some circumstances? If not what is special about cells that never produce cancer? Why do some cells produce cancer relatively frequently while others do not? How well is this predisposition toward or against cancer development understood?
Wonderful discussion and a very nice question,Just adding some points to the discussion. With the development in high throughput techniques and specific molecular, biological, clinical research coming together, many aspects of cancer initiation-formation, biology, progression are unravelling such as cell type specificity, stem cell origin of cancer, transcriptions factors for pluripotency vs differentiation, genetic errors and mutations, epigentic and immunological factors along with socioeconomic factors, ethnicity, and geographical location (diet) regarding the incidence and understanding of cancer.
I think the cells that are most prone to cancers depends on their exposure to the hits involved in cancers and also their proliferative and differentiation status.
1. So epithelial cancers are the commonest such breast, prostate, lung, colorectal.
2. then Melanoma, Lymphoma, Leukemia, the list varies with the location in the globe, ofcourse.
3. Neuoblastomas is a rare cancer that occurs in the children, while most brain tumours develop from cells that support the nerve cells.
4. And many rare tumours that are found in the 'rare list' are very specific such as Merkel cell skin cancer, Angiosarcoma of the heart. Very well differentiated cell types are may be not switched back to pluripotency easily or may be these cell types not easily exposed to triggering mechanisms as are the cancer stem cells.
I would like to bear in mind the basic cell types and the location of their stem cell type in our body keeping in mind their normal functionality and derailment from it, by DNA damage and also their normal proliferative and apoptotic signals (as the damaged cells are may not be cleared) regulates how common or how rare a tumour may be. Ofcourse other factors mentioned above do come into play.
How a stem cell becomes a cancer stem cell having the multipotent capacity by acquiring genetic modifications is vital, as clonaity of cancer has shown that origin of the tumour goes back to a primary cancer stem cell. It is important to be hit by one or multiple mutations by triggering agents in the environment (bacterial, viral or toxic) and the cells proliferative capacity allowing it not to be able to repair the damage or other enzymes or molecules in the repair pathways being ineffective. Also, epigenatic mechanisms may come into play along with the genetic aberrations in the mutihit process of cancer formation and progression.
The refs below in cancer biology, progression and pluripotency factors may help further understanding.
2.Cell. 2006 Aug 25;126(4):663-76. Epub 2006 Aug 10.
Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors.
Takahashi K1, Yamanaka S.Following
- Valentine Comaills added an answer:Does anybody have a good antibody to detect human cells in mouse xenograph model?
my cells are human breast cell line GFP/luc but my GFP signal is very low. I cannot find a good anti-GFP to detect it (I also tried TSA amplification, it is not working). Anti-Luciferase antibody from abcam is very unspecific. I tried anti human mitochondrial MAB1273B from millipore and do not get signal. I am thinking to buy the MAB1281 from millipore anti nuclei human, but I read bad comments about this antibody. Any suggestions? Thank you very much in advance.
when I say overfixed, it is because I have a lung metastasis, that clearly is from my primary site (confirmed by pathologists with H&E stain), but i cannot stained it for my antibodies, I fight as crazy for it, but nothing... some collaborators also tried to do FISH on it and cannot do it... I put my sample in formalin overnight, but it seems that this piece get overfixed..(other sample were fine). but if you already stained with other thing your sample and have signal, your sample should be perfectly fine... I think the MAB1273 is weak so need to have a good sample to begin with.
- Holger Zeitler added an answer:Is there a role of CA 15-3 as a biomarker for breast cancer in the surveillance of a properly selected group of ”high risk” women?
As a radiologist, interested in cancer imaging, i came across a publication
(Atoum, 2012), that could show correlation between elevated CA 15-3 and stage II-III breast cancer.
Of course CA 15-3 cannot detect early stage breast cancer and is therefore not recommended in screening (Duffy, 2006).
But sometimes it can be challenging to find a 2-3 cm diffusely infiltrating breast cancer in asymptomatic - especially premenopausal - women with dense tissue (Buist, 2004. Kolb, 2002).
A serum marker might be helpful to select patients for further evaluation, e.g. Breast-MRI, tomosynthesis or ultrasound, in order to find “medium size” breast cancers, that otherwise would go undetected by mammography for quite a while with worsening prognosis.
Hi Christina, thank you for that interesting information:
imaging methods might be less sensitive than CEA and CA-15-3 to predict recurrences in advanced breast cancer.
a little bit like mammography screening in women with very dense breasts,
or ultrasound screening for HCC detection in patients with liver cirrhosis:
not 100 % sensitivity and specificity ....
there is a paper, which may be interesting in that context: Alpha-Fetoprotein Measurement Benefits Hepatocellular Carcinoma Surveillance in Patients with CirrhosisFollowing
- Ana Rita Pedrosa added an answer:Which IHC markers are the best to show epithelial-mesenchymal transition on FFPE tumor samples?
I testing this on in samples of normal skin, actinic keratosis, in situ and invasive SCC of skin. I used Vimentin, E-cadherin and N-cadherin, but I have problems with interpretation of my staining results. Vimentin is quite intense and easy to interprete. E-cadherin in invasive SCC is pale or there is no staining in samples that do not show vimentin expression. In in situ lesions is focally lost (in actinic keratosis in regions where atypical cells are). N-cadherin is pale and seen only in few tumors. Different authors used different combination of markers. I was wondering which one or which combination is enough and safe to say wheter EMT is present or not?
I used successfully, E-cadherin and the EMT transcriptions factors, Snail and Slug. The latest factors are seen as small dotted points inside the tumor cells. In my case, frozen-mouse prostate samples, the areas which exhibited tumorigenic transformation with a considerable degree of dysplasia had loss of E-cadherin and positive staining for the mesenchymal factors referred. In the skin you will probably have a lot of vimentin staining, due to the presence of myofibroblasts?
Hope this helps you...Following
- Neeraj Verma added an answer:What is the scientific and most acceptable way to give doses of carcinogenic compound to a mice dermally?
In my experiment I'm giving the doses of DMBA/TPA, with my compound of interest, what would be the best and most widely accepted scientific way to give doses and treatments?
1: Trim the upper dermal hairs and give the doses with the Pipette?
2: Remove the hair with the hair removal creams and then apply the doses?
3: What could be other suggested way?
Either you can use hair removal cream.
Apply the hair removal cream (VEET) carefully on the mice skin and then slowly take out the hair using cotton.Following
- Sinan Ibaguner added an answer:What are the clinically used biomarkers to detect Diabetic Pancreatic Carcinomas?
There are many biomarkers for the detection of pancreatic cancers, leading the pack is CA 19-9 whose sensitivity and specificity is less than optimal. In clinical settings, are there any other markers that has proved more useful in detecting diabetic pancreatic cancers?
Particularly in heavy drinkers &/or smokers screening of ESR & CRP must be done periodically in order to diagnose pancreatic cancer at treatable stages.Following
- Shyam Bandari added an answer:Any suggestions on the problems with the Western blot analysis on Myeloma patient serum derived exosomes?
I have Isolated exosomes from myeloma patient serum using Exoquick kit (SBI)..and I confirmed the size using Nano sight (50 to 200 nm)..Till this point all fine but I have an issues performing western blot on these samples, when I add WB loading buffer and heat the sample...sample is getting viscous (gluy)..so I was unable to proceed further ....does any one have suggestions to circumvent this problem ??
Thank you all.... I have diluted my sample and performed the western blot.. and the results look fine, I could see the protein of my interest.....once again Thank you allFollowing
- Peter Kloehn added an answer:Which antibodies attached to gold nanoparticles are used to detect breast cancer?
Gold nanoparticles synthesized by Citrate reduction method and loaded with anti cancer drugs are used to target cancer cells. Which antibodies are used for detection of these cells and how these antibodies will be attached to the surface of AuNPs?
Best to use therapeutic antibodies used to treat breast cancer, as these antibodies are FDA approved. Commercial antibodies are not validated and may show substantial off-target effects. ERBB2 is overexpressed in breast cancer tissue and can be targeted by Trastuzumab and Pertuzumab. Also, the EGFR is overexpressed in breast cancer and can be targeted by Cetuximab, Panitumumab, Nimotuzumab and 806.Following
- Sunil Badve added an answer:Are there some complete and authoritative databases for cancer biomarkers?
As we know, it's a time-wasting work to curate biomarkers of some specific cancers from massive literature and they may be incomplete for us. Therefore, I want to know whether there are some complete and authoritative databases for cancer biomarkers? By the way, noncommercial and publicly available databases may be better.
there are others such as KM plotter - which are tumor site specificFollowing
- K.Kamil Reza added an answer:Why are long non-coding RNAs are important for cancer diagnosis?
I would like to know about the non-coding RNAs as cancer biomarkers
Thanks for the answersFollowing
- Svetlana Boudko added an answer:What immunohistochemical markers would you use to define a Granular cell tumor of breast as benign or malignant?
Notwithstanding the Smith-Fanburg criteria, what immunohistochemical markers would you use to rule out malignancy?
I mean Granular cell tumour (breast), can tubular structures be seen there?
- Henning Zelba added an answer:Can anyone suggest a reliable glioma marker?
We're looking for a nice marker to detect tumor cells within glioma tissue. The tissue will be dissociated into a cell suspension. After that, we want to stain the suspension with a mixture of antibody-conjugates for flow-cytometric analysis to get an idea of the cellular composition of the tumor...
Can anyone suggest a marker (either extra- or intracellular) that is only/mostly expressed by tumor cells?
Thanks Christopher!!!! Nice discussion already. I will comment here as soon as we have collected a few samples...Following
- Jan Voskuil added an answer:Does anybody know of a good human Snail and Twist antibodies for IHC?
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!
I completely sympathize! Publishers need to demand authors to specify the catalog numbers. Everest Biotech has a goat peptide antibody shown fit for IHC in mouse: EB07405. However, batch has changed and the confirmation came from the former batch (another thing to worry about!). You should give this one a try and if you get stuck let us know.Following
- Björn L.D.M. Brücher added an answer:What are the consequences differences of plasma DNA and DNA from HCC tissues?
What will be the consequences out of this?
Extract by Florent Mouliere / Montpellier and Nitzan Rosenfeld / Cambridge:
Circulating tumor DNA (ctDNA) is now widely investigated as a biomarker in translational and clinical research. However, despite the growing field of clinical applications, the biology of ctDNA remains unclear. In trying to learn about the origins of ctDNA, nature provides us with very few clues. One of the important accessible parameters is the size of those DNA fragments. In addition, a well-informed model of these sizes and biases can help design more efficient and accurate diagnostic methods. In PNAS, Jiang et al. take an important step in that direction.
We used massively parallel sequencing to study the size profiles of plasma DNA samples at single-base resolution and in a genome-wide manner. We used chromosome arm-level z-score analysis (CAZA) to identify tumor-derived plasma DNA for studying their specific size profiles. We showed that populations of aberrantly short and long DNA molecules existed in the plasma of patients with hepatocellular carcinoma. The short ones preferentially carried the tumor-associated copy number aberrations. We further showed that there were elevated amounts of mitochondrial DNA in the plasma of hepatocellular carcinoma patients. Such molecules were much shorter than the nuclear DNA in plasma. These findings have shed light on fundamental biological characteristics of plasma DNA and related diagnostic applications for cancer.
The analysis of tumor-derived circulating cell-free DNA opens up new possibilities for performing liquid biopsies for the assessment of solid tumors. Although its clinical potential has been increasingly recognized, many aspects of the biological characteristics of tumor-derived cell-free DNA remain unclear. With respect to the size profile of such plasma DNA molecules, a number of studies reported the finding of increased integrity of tumor-derived plasma DNA, whereas others found evidence to suggest that plasma DNA molecules released by tumors might be shorter. Here, we performed a detailed analysis of the size profiles of plasma DNA in 90 patients with hepatocellular carcinoma, 67 with chronic hepatitis B, 36 with hepatitis B-associated cirrhosis, and 32 healthy controls. We used massively parallel sequencing to achieve plasma DNA size measurement at single-base resolution and in a genome-wide manner. Tumor-derived plasma DNA molecules were further identified with the use of chromosome arm-level z-score analysis (CAZA), which facilitated the studying of their specific size profiles. We showed that populations of aberrantly short and long DNA molecules existed in the plasma of patients with hepatocellular carcinoma. The short ones preferentially carried the tumor-associated copy number aberrations. We further showed that there were elevated amounts of plasma mitochondrial DNA in the plasma of hepatocellular carcinoma patients. Such molecules were much shorter than the nuclear DNA in plasma. These results have improved our understanding of the size profile of tumor-derived circulating cell-free DNA and might further enhance our ability to use plasma DNA as a molecular diagnostic tool.
Jiang P et al.: Lengthening and shortening of plasma DNA in hepatocellular carcinoma patients. Proc Natl Acad Sci U S A. 2015 Feb 2. pii: 201500076.
well pointed out.
We also have this discussion at the web group of theTheodor-Billroth-Academy on LInkedin and Reinhold Kiehl, Hossein Rahmati Roudsari and Jan Voskuil made very important points and I try summarizing those:
-tumor markers as CEA or CA19-9 should be used for follow-up-never for making the diagnosis, as the overall accuracy is too small. Further tumor markers are expressed proteins on surface membranes and we learned from epithelial cysts that such can mimick a cancer, e.g.in spleen cysts very high CA-19-9 had been observed without any association of any cancer, nor during follow-up
Therefore, we by now do not know
- the influence and value and accuracy of detectable DNA
-when the best time is measuring it and how the values are influenced
-how storing would be best and how the interobserver variability might be
-when free DNA is measurable, how do such values differ after treatment
-are they proven being related to the observed cancer or assumed to be
-microRNA#s had been observed in ling cancer patients assuming having impact on spread and even cancer development but again: assumed!
-to my knowledge no standard protocol is accepted or suggested determining free DNA so far
Additionally Ijaz Jamall added a valuable insights deepening he comment from Hossein Rahmati Roudsari and Jan Voskuil (copy and pasted):
Ijaz Jamall: "I agree with Dr. Rousdari and Jan: one key factor to consider in measuring anything in the blood is its half-life and how to "normalize" the thing being measured - per ml blood or serum, per g protein, etc. because essentially we are measuring a concentration as opposed to a mass and dilution and binding kinetics or changes in hydration or albumin content can make huge a difference. In fact, diurnal variation can itself make a huge difference"Following
- Nilgun Tasdemir added an answer:How do you recognise epithelial-to-mesenchymal transformed (EMT) cancer cells in clinical samples?They should have reduced or absent epithelial characteristics, so how do you discriminate them from authentic mesenchymal cells?
I am also interested in looking at this in human breast tumor tissues. Does anybody know of good human Snail and Twist antibodies that work well for IHC on FFPE samples? Thank you!Following
- Ladislav Burysek added an answer:Expression of PSMA in human vs. canine prostate: a useful biomarker in PC studies in the canine model or NOT?I've found two groups of articles that state different conclusions.
According to Aggarwal S, Ricklis RM, Williams SA, Denmeade SR, "Comparative study of PSMA expression in the prostate of mouse, dog, monkey, and human," (Prostate. 2006 Jun 15;66(9):903-10), "PSMA is not expressed in any significant amount in the prostates of mouse, beagle dog, or macaque monkeys in this study but is expressed in high levels by human prostate. These non-human species, therefore, are not suitable toxicologic models to assess prostate damage from PSMA-activated intraprostatic prodrug/protoxin therapies."
However, in the more recent article of Schmidt S, Fracasso G, Colombatti M, Naim HY, "Cloning and characterization of canine prostate-specific membrane antigen," (Prostate. 2013 May;73(6):642-50) it's stated that "We demonstrate that canine PSMA reveals similar characteristics to human PSMA rendering this protein useful as a translational model for investigations of prostate cancer as well as a suitable antigen for targeted therapy studies in dogs."
Another recent article below appears to support PSMA as well:
Lisa Y Wu, Jacqueline M Johnson, Jessica K Simmons, Desiree E Mendes, Jonathan J Geruntho, Tiancheng Liu, Wessel P Dirksen, Thomas J Rosol, William C Davis, Clifford E Berkman, "Biochemical characterization of prostate-specific membrane antigen from canine prostate carcinoma cells," (Prostate, 74:451-457 (2014))
So, can somebody clarify if PSMA can be indeed a useful biomarker to target in the PC canine model? Thanks!
GFP labeled prostate cancer markers: http://www.protean.cz/en/recombinant-proteins/cancer-markersFollowing
- Ladislav Burysek added an answer:What are the simple biomarkers for prostate cancerUsing blood or urine
GFP labeled prostate cancer markers: http://www.protean.cz/en/recombinant-proteins/cancer-markersFollowing
- Ahmed Kotb added an answer:Besides PSA and DHT levels are there any other (specific) biomarkers for Benign Prostatic Hyperplasia (BPH)?
I'm conducting a research on the Chemoprevention of testosterone induced BPH on Rats using some food plants.
I believe there is nothing but PSA and DHTFollowing
- Serge Grabtchak added an answer:Do you know any biomarkers except PSA for early detection of prostate cancer?
Can anyone recommend biomarkers which are associated with prostate cancer and which may may usefully in its diagnosis? Because PSA is having issues with sensitivity as a biomarker.
What about PSMA? Has anybody used it? Pros and cons?Following
- Stefano Ciciliot added an answer:Does anybody know antibodies for single use?
Everybody knows that antibodies are so costly, ranging from 150-300 USD/antibody.These are available in 100-500 ul quantity. I want to test a cell signaling pathway, for which i need 5-10 antibodies, in 10-20 ul qunatity. I am not sure whether my idea about that specific pathway will work or not. That's why i am not dare to order all antibodies for this new experiment. A thinking comes to mind that may be there are some companies which provide antibodies for single experiment in minute quantity like10-20 ul. But i am not sure. Can anybody help me? Your comments will highly appreciated.
have you ever tried to give a look at Developmental Studies Hybridoma Bank (DSHB)? They have a good panel of monoclonal antibodies, and they are really affordable (35$ for 1ml supernatant, 55$ for 0.1ml of concentrated antibody).
- Tahmina C Islam added an answer:Can Herceptin overcome primary Cetuximab resistance in metastatic colorectal cancer?
KRAS,NRAS,BRAF wild type colorectal cancer can response the anti-EGFR therapy using cetuximab or panitumumab. However, in some cases such as Her2 or MET amplification there will be an resistant to anti EGFR therapy although tumor has KRAS,NRAS and BRAF wild type genotype. If there is a polysomy in chromosome 17(Her2:CEP17 ratio 1, however there is a increasing number of chromosome 17 such as 3:3,4:4), using FOLFIRI+Cetuximab+Herceptin can overcome EGFR resistant in metastatic colorectal cancer?
Very interesting discussion, I would just like to add besides the discussions above, one may also keep in mind the PI3K, MEK, AKT mutations that may be involved and molecules of other alternative or additional pathways that may be involved in resistant metastatic colorectal carcnomas. The article below may be of help.
- Alexander Zhavoronkov added an answer:What is a strategy and accurate pipeline of cancer diagnostic biomarker identification?
I think it is an ancient and classic question for cancer diagnostic biomarker identification. There should be some mature protocol or pipeline to discover such biomarkers for cancer screening and diagnosis, which include the discovery stage, validation stage, sample size estimation and so on.
Do you have any solid suggestions or articles to recommend on this question?
Shincheng, you may consider narrowing your question down to a specific cancer type.
Markers for hematologic tumors will be drastically different from those of solid cancers. Melanoma and most skin cancers will have very different diagnostic markers.
In the case that you are looking for broader references, please consider the following books:
When considering which books to review (there are thousands), look for most recent texts by reputable authors, since the field is changing at unprecedented rates.Following
- Michele Doughty added an answer:Any advice on prostate Cancer cell lines, genome portal?
Hi, I am looking for a source to get copy number data for prostate cancer cell lines such as PC3, LNCaP, DU145 , ..etc.
I checked Oncomine but i can not find these data. Share plz if you have a clue.
You may want to read this article related to the genome and prostate cancer to get a better understanding of gene alteration and copy data. Also review the National Institute for Health could provide assistance with your question http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000447.v1.p1
- Dimitrios Zardavas added an answer:What are the mostly used breast cancer biomarkers? What's your opinion about erbB-2?
I am planing to detect breast cancer by some electrochemical means and for that I have to select some bio-markers.
in terms of biomarkers with validated clinical utility, the established triplet would be ER/PgR/ErbB2 (HER2). All three bear both prognostic and predictive relevance, since:
- the first two hormone receptors are associated with positive prognostication and predict for benefit derived from endocrine treatment
- erbB2 (HER2) is a marker of poor prognosis and is associated with prediction of benefit from HER2 blocking agents (4 such agents approved in the setting of breast cancer: trastuzumab, pertuzumab, lapatinib and TDM1).
Ki67 has also prognostic relevance (higher proliferation rates associated with aggressiveness of the disease) and some predictive relevance, since higher Ki67 levels have been associated with chemosensitivity.
About Cancer Biomarkers
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.