Science topic

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
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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?
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thank you for answring my quesion dear Dr Erum Zafar
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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!!!
regards
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Dear Dr Mohammed,
I also suggest you to read these recent articles:
Best regards,
Pr Hambaba
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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.
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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
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Hello,
SV40 is not considered an oncogenic virus in this review:
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?
Thanks!
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Please have a look at the following RG link.
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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?
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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.
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Hi everyone!
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?
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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.
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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?
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" Vimentin is a cytoskeleton intermediate filament protein present in cells of mesenchymal origin; this includes leukocytes, endothelial cells, and smooth muscle cells."
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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 !
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Oncology rule: Go for the money (i.e. tissue diagnosis). Oncologists will refuse to see a patient for management unless the tissue diagnosis is available.
A DICTUM USED BY ONCOLOGISTS IS "NO TISSUE, NO ISSUE".
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.
Please have a look on the links below to these articles on tumor markers in general and the CA 19-9 in particular.
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Hi all!
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!
Best,
Brenda
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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.
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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?
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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.
I hope it will help you. If I went wrong please do let me know.
Regards
Saurabh
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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 
thanks
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Which colorectal cell lines that has c-Met overexpression or amplification, dose anyone has any related literature please send me
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H820
MET amplification occurs with or without T790M mutations in EGFR mutant lung tumors with acquired resistance to gefitinib or erlotinib
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"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
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Joe Graymer
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)
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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.
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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
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tools or servers for determining important biomarkers in many cancer, for example, glioblastoma multiforme (GBM) or breast cancer and others??
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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.
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I'm conducting a research on the Chemoprevention of testosterone induced BPH on Rats using some food plants.
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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.
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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
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Hey guys,
I have been working with breast cancer biomarkers HER2, ER, and PR. I have tried to look up charges for those proteins. Just wondering if anyone knows if HER2, ER or PR are positively or negatively charged proteins. Thanks!
Diya
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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).
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Dear All,
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.
Christophe
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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.
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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!
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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
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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!
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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.
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Nature Webcast
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?
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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!!
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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.
http://science.sciencemag.org/content/sci/359/6378/866.full.pdf
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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.
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i went to know the biomarkers level of breast cancer in saliva,
if any one worked in this area ?
thank you
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good evening zahra, i am not sure! , i am looking forward to know those bio-markers and their levels in saliva
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Hello,
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?
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    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, 
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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
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@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???
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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.
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Thank you Dr. Islam, ICGC was also great help for me.
Appreciate it.
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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? 
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Try xena.ucsc. You will fall in love with it.
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Is there any somatic mutation gene panel for detecting breast cancer?
I already know there are Germline mutation gene panel for Breast Cancer
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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....
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I have also done few biomarker based experimental studies.
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What is your Suggestion
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what is best treatment for patient with CA lung with pleural effusion and EGFR mutation positive ?
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 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.
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Hi,
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.
Best,
Martyna
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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
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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?
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Thank you fro your suggestions!
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Dear folks,
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 !
Best regrads,
Jeong-Hwan.
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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. 
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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?  
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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
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Thanks.
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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.
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Protein extraction kit for dogs.
Molecular characterization of proteins (Proteomics)
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Thanks Prasanth
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I did profile of miR and company said they choose a panel of high confidence miR. What does this mean? 
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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
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Required to have some papers related to environmental impact over cancerous cell singling.Very simple and easy to understand for my internship work. 
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Dear all, 
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?
Thank you
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Thank you Dr. Aline C Planello
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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.
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Thanks-Waqas. It is very helpful. Best wishes.
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Are there new drugs/protocols in the treatment of serous (sporadic p53) endometrial carcinoma ?
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I am interested in lentil lectin sepharose glycoenrichment methods protocol.
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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.
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I am preparing presentation for my upcoming conference in India. Anyone help me to provide information about difficulties, challenges in using miRNA probe for cancer diagnosis. Thanks in advance
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Dear Gnanasekaran
You can use from FOBT for cancer diagnosis in colorectal cancer
Best wishes
Mohammad Amin
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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?
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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.
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I wanted to know the availability of Imaging Flow Cytometry in India or Abroad. Also, I need to discuss some features of experiments with it. Any expertise??
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Mr. Arvind,
I already enquiry to those labs as they don't use Imaging Flow Cytometry.
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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.
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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.
Best
Baki
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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
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In different grades of breast cancer cell line , what are the reference genes/proteins can be used?
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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. 
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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.
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Hello everyone
I want measure micro-RNA in blood plasma of patients with heart failure, can I use of cel-miR-39 as a control?
thanks
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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
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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!  
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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).
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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?
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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/
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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.
Thank you
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Overall, PSA is the most widely used.
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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).
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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.
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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.
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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.
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Hi,
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?
Thank you
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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.
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I want to find a high expression and low expression colorectal cell line to culture
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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!
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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.
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Hi, I am looking for information about how to use FACS to analyze mouse tumor stromal cell? What markers should I use
please tell me which FACS antibody is good for detecting stromal cells. Thanks 
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 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.
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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.
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 which sequence did you order?
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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?
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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?
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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. 
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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.
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Working plate form.
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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...
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myeloma stem cell
isolation
sorting
culture
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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. 
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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 .
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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.
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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.
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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.. 
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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)
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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.
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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.
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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.
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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.
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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?
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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.
Thanks
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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
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Sensing with the help of aptamers.
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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
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Hello everyone,
Do you know what is the level of MMP-9 in the breast cancer tissue?
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Poštovana Danijela, 
Interesantne podatke možete naći na linku:
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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?
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First do IHC, if the link is confirmed, then carry on with ELISA or WB
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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.
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sorry no
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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.
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Use link below to find splice variants of any human or mice gene. I quick search revealed 14 variants of human BRCA1 gene.
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We are following HR and NHEJ pathway. Want to know the assays and techniques to go ahead
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Dear JK,
The attached file is a recent published review that covers the answer to your question.
Effective Biomarkers and Radiation Treatment in Head and Neck Cancer
Thomas J. Ow, MD, MS; Casey E. Pitts, BA; Rafi Kabarriti, MD; Madhur K. Garg, MD, MB, BS
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.
(Arch Pathol Lab Med. 2015;139:1379–1388; doi:
10.5858/arpa.2014-0574-RA)
CONCLUSION
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
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For example what proteins and receptors are produced in normal breast cells and malignant cells.
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you can run protein antibody array and compare the expression in normal versus malignant tissue
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Hello everyone.
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?
Thank you!
Connor Hoge
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“NF-κB and STAT3 – key players in liver inflammation and cancer” maybe this review could have some help for you.
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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?