Breast Cancer - Science topic

There is the BOMET trial that just finished recruitment. It is the 2nd trial of the same Author from Turky who presented data on primary surgery for stage 4 breast cancer 4 years ago at ASCO

We had experience of working with oncosurgeon. The most important thing we had to deal with was the timing. Sometimes, our fellow had to wait for a tissue more than 12hrs. We don't have -80 fridges at tissue collection site and don't have that much facilities. For tissue sample preservation, RNALater is a blessing for us. Part of the tumor tissues was kept for pathological tests and the rest was given to us for molecular analysis. Tissue sample was stored in RNALater containing tube immediately after collection, transported to lab in an icebox, and stored at -20C.

Hi Sir,

You can check gene expression at protein level using Human Protein Atlas (https://www.proteinatlas.org). Also, NCI Proteomic Data Commons can be explored (https://pdc.cancer.gov/pdc/)

Hello Raid M. Al-Salih

Tumor markers, also called serum markers are substances found at higher-than-normal levels in the blood of cancer patients. Serum biomarkers are especially appealing for the potential to detect disease progression or response to treatment.

In breast cancer care, three tumor markers -- cancer antigen 15-3 (CA 15-3), cancer antigen 27.29 (CA 27.29), and carcinoembryonic antigen (CEA) -- have been used to help monitor metastatic breast cancer.

National Comprehensive Cancer Network (NCCN) and American Society of Clinical Oncology (ASCO) guidelines recommend serial monitoring of CEA, CA 15-3, and/or CA 27-29 in metastatic disease; particularly, an elevation of 20% to 30% in any of these markers in addition to clinical exam can indicate treatment failure.

National Academy of Clinical Biochemistry (NACB), and European Group on Tumor Markers (EGTM) recommend measuring CEA, CA 15-3, and CA 27-29 for postoperative surveillance, even without evidence of progression.

The EGTM alone recommends preoperative measurement of CEA or CA 15-3/CA 27-29 in combination with established factors to aid in determining prognosis.

Best.

Haddadi Saïd , true for reconstruction, can this extend or be extended to only simple mastectomy or radical one ,without rec?

Where we can download the BCDR mammo database (especially the Digital part of the collection) ? No one seems to answer from the official site. Anyone who can provide a download link?

thank you.

DNA repair pathways are involved in maintaining genetic stability and, in this respect, repair factors are to be considered as tumor suppressors. This applies to the BRCA1/2 genes, for which inherited mutations in one allele predispose to cancer. There is no paradox in the fact that PARP inactivation leads to the death of BRCA-deficient tumor cells. In this case where homologous recombination is impaired, cell survival relies on PARP-dependent backup repair processes. Apparently, here, PARP promotes tumor development but even in non-tumor HR-deficient cells, survival would depend on PARP. We just take advantage of this synthetic lethality phenomenon due to HR deficiency to kill cancer cells.

Anyway PARP functions are not restricted to DNA repair and it is possible that in some peculiar circumstances PARP may rather promote tumorigenesis.

Ellen A G Chernoff Dear Professor Chernoff, thank you so much for the advice. I did not know about these tools. I will check them.

Hello Gongli Cai

There are techniques that have been developed to detect and identify MMPs in various samples. Enzyme linked immunosorbent assay (ELISA) and Western blot require the use of antibodies targeted to the MMP of interest.

I would suggest you use gel zymography which is extensively used to detect MMPs in many cell types and tissues as well as in most bodily fluids.

You may follow the protocol described in the article attached below.

Best.

I found these papers:

Thank you Susan C Hubchak for your useful reply. I'll definitely try like you said.

Also, see the RG link below.

If you ate well grounded in the course of your MPhil Molecular Biology and Biotechnology, there may not be need to go for another MSc in Molecular Biology and Biotechnology

I advice you proceed to doing PhD in Molecular Biology and Biotechnology except you know within yourself that you not well grounded enough and this depends on how truthfully you have evaluated your competence

Best wishes

Oh, it's great to hear you from sir Robert Boer. I already cited your work multiple times.

Well, I adopted case-control and also cited some limitations of it from your paper.

K. Sujathan Thank you very much!

Hello. Did you get the code?

Kindly see also the following useful RG link:

Sorry for the late response. I would like to correlate with H&E. Can you please share that? Thanks

normally people starve at low concentration 0.2% serum for 12h or sometimes 24h

I will respond to this question in french. in my thesis, the sratician calculate the "taille échantillonale" en se basant sur les résultats de la sensibilité (Se) et de la specificité (Sp) retrouvés dans la littérature médicale.

nSe= 4 x Se x (1-Se)/i×i

nSp= 4 x Sp x (1-Sp)/ixi

N= nSe+nSp

i étant la précision que l'on souhaite obtenir. Elle varie de 5 à 10%.

Good luck.

Thanks Saubhik Sengupta...

Researchers have discovered that breast cancer cells are more likely to jump into the blood when people are resting. The revelation is relevant because cancer is at its deadliest when a tumour’s cells worm their way into the bloodstream and travel to a new location in the body to set up shop — a process called metastasis. It doesn’t mean that people with breast cancer should avoid sleep — that’s bad for you. But it does give clinicians a better understanding of how to track these rogue cells. “The first lesson for me is that the time of day you take a blood sample can give you misleading information”, says cancer biologist Chi Van Dang...

Thank you

@Malcolm Nobre

You can assess the normality of your data's distribution using skewness and kurtosis tests.

If your data fit the assumptions of the appropriate parametric test (for example: https://www.statology.org/t-test-assumptions/), then you probably should use that test. You can always substitute a non-parametric test for a parametric test, but you typically will lose some statistical power. However, if your data violate the assumptions of the parametric you will need to use the non-parametric test.

hi,

the white layer on the flask is debris of dying cells. Are you sure, that the flasks are Tissue culture grade/ coated for adhesion cell culture? For me it looks like an attachment issue and all non-suspension cells die fast in the wrong type of bolltes

Sven

Both collagenases and cytokines are mistakenly regarded as facilitators of metastatic spread of tumors. Tumor cell itself has the remnants of gene regulation and the adjacent tissues are partners in the upregulation of estrogen signaling and DNA restoration in tumors. Collagenases help the arrival of cytokines and other mediators aiming the restoration of the genomic machinery in tumors and self directed death. Cytokines activate aromatase enzyme for stimulation of estrogen synthesis, while an increased estrogen level silences inflammation and improve DNA stability even in tumor cells. In conclusion; there is no parallelism between the activity of collageneses or cytokunes and tumor spread.

Concerning cancer research, Journal of Oncology and International Journal of Molecular Science provide good possibilities for publication of innovative works.

Giuliana D Noratto came across a question and answer typically not same but somehow linked to your question so felt like sharing the answer and you can see how Dr S J Malik https://www.researchgate.net/post/Problem_with_4T1_Tumor_Model_Development-Can_anyone_help

This is for your refernce

If you administrated your nanoparticles locally (intrtumor injection) , I think you needn't design the specificities or targeted strategies of your drug delivery. Because from tumor biology perspectives, the aggressive cancer cells are always infiltrating into surrounding microenvironment with some physical or immune barriers. Therefore, even if you treated the cancer cells by monoantibodies, you can't kill the tumor totally.

However, if your delivery strategies are intravenous injection, tageted therapy is the most important principle that you must take into considerations. So, in this context, my suggestions are that what kind of tumor you are goning to treat decides what antibodies you are attaching. As is known to all, breast cancer has less than three kinds: ER+, HER2+, and trible negative (luminal). I suggest you could widen your antibody choices for HER2+ breast cancers. Do the nanoparticles have a good ability to load Antibodies? What's the relationship between your breast cancer cells with your mesoporous NPs, drugs, and Antibodies? ...

Dear Dr Sing,

To find the function of proteins you can use uniprot database or genecard.

Before molecular docking, you should check the druggability of your protein by pockdrug. By molecular docking and MD you can find best compounds

Yes, neoadjuvant systemic therapy is now considered standard practice for following subsets of breast cancer patients:

1. Inflammatory breast cancer

2. cT4 disease

3. cN2 or cN3 disease

4. Operable breast cancer with triple negative or HER2 +ve molecular subtype with cT2/N+ or higher disease stage

5. Large primary tumor relative to breast size, or when cN+ likely to become cN0 with neoadjuvant systemic therapy to facilitate breast conservation

The most recommended method is to use estradiol pellet to support growth of MCF7 cells, but implanting cells with materigel can work (though low tumor formation rate) which is more cost effective.

Also, I found these links that may helpful in related to this thread:

In my opinion informed patient decision would be the most important thing.

To control direct tumor response after introducting drug chemothrapy or target thearapy.

TNBC, HER2+ are different sub-types with different signaling pathways (though most pathways in all cancers are common). Since they are 2 different subtypes based on the presence or absence of different protein/receptors their signaling mechanism will be different.

when you talk about BCSC you need to specify the source, which is important.

the patient can have low HER2+ and TNBC (is another emerging sub-type within TNBC and have a low level of HER2+), so it is possible.

Liquid biopsy techniques can provide real-time information regarding patient staging (metastatic vs. nonmetastatic) and the molecular profile of the tumor. Moreover, liquid biopsies can be repeated with the desired frequency for close monitoring of progress and treatment

if you are looking for nucleotide sequence... plz go to protein database .. if you want normal sequence ... if you want mutated then OMIM or other ... and wanna compare , i think BLAST is the best tool for comparison

Human breast cancer includes a highly diverse set of diseases and is classified in to at least 6 distinct clinically-relevant molecular subgroups - luminal A, luminal B, HER2+/ER-, basal-like, normal breast-like, and the most recently recognized claudin-low. It is clear that at the molecular level, each breast cancer subtype displays distinct gene expression profiles, and exhibits significant differences in response to therapy and patient outcome

So I will preface this by saying I work for a completely different company just so that is clear but I've run into a few groups with a similar problem and it seems like the software itself needs some adjustments. This is likely a back end fix/code rewrite that Nexcelom and companies like it need to do, to make the systems work more effectively across a variety of assays and cell types.

On that note Jennifer, depending on how often you and your team run these assays (mammospheres, colony, organoid, etc) there are other systems which are more dedicated to the task are doing (ie counting and sizing), the GelCount being the one I know. Not suggesting this is a fix for your problem but just a different solution. All the best.

Also see the following useful link for more insight.

thank you for answring my quesion dear Dr Erum Zafar

Hi,

I don't know for MCF7 specifically, but the concentration used for different cell types are quite similar:

0.01% for RBCs: https://www.pnas.org/content/pnas/114/16/4225.full.pdf

0.01% for CH27 result in half-max. stiffness increase: DOI:

Hello Giermin Sahagun

You can use real-time luminometry to study changes in gene expression. The investigators generated luciferase reporter systems to track BMAL1 and PER2 expression in real time.

Please refer to the research article attached for the detailed protocol.

Good Luck.

اسباب كثيرة ينبغي عليك البحث عنها

Dear Majdi,

Even if you are going to start at 1:5 ratios of the two drugs when you prepare the NP, you most likely won't end up with a final ratio of 1:5 encapsulated. Thus you will need to optimize the protocol to produce the final NP with a ratio of 1:5 encapsulated. Then simply you inject an equilavent dose of drugs.

For example, if for free drugs you will use 1 and 5 mg/kg respectively, you will have to inject the same dose with the nano ( a concentration of nano that has 1mg/kg of drug 1 and 5mg/kg of drug 2). For this, it is critical to produce the nano with 1:5 final ratio.

I hope this helps.

Regards

Francesco

Please contact https://www.researchgate.net/profile/Mohamed-Hassan-36

Hi Manar Serageldin,

I've been facing the same problem too but with a different kit called Macherey-Nagel Total RNA Isolation from FFPE. I was trying to extract RNA from formalin-fixed paraffin-embedded samples of colorectal cancer. For the first few attempts in extracting RNA from the FFPE tissue, I followed exactly what the protocols say, where it stated to incubate the FFPE with proteinase K in the lyse step for only 15 mins which gave me very low RNA concentration (~10-40), and also the 260/280 ratio. However, after troubleshooting I got to know that we can optimize the duration of incubation from 15 mins up to 3 hours with proteinase K (overnight digestion can also be done, but up to 3 hours is the optimal digestion time) depending on the size and thickness of samples and also by looking at the portion of the undigested sample. So I started to incubate my samples for approximately 2 hours and I managed to get a high amount of RNA concentration (~500-1500). However, for the 260/280 ratio, the best I have gotten to date is 1.9. Maybe you should try to increase the washing steps to get a good ratio of 260/280 and 260/230.

I hope this helps.

All the best to you.

Dear Yongzi

I am not sure that your conclusions can be accepted without further experiments.

For example,

do cells express MDR proteins,

or the drugs are weak bases that can be easily ionized

or what chemical interactions occur between the drugs.

Answering these questions should precede the statistical representation.

Kind regards.

Tomas

Hello Shahina Akter I am not sure what you are asking Since baseSpace gave you the final vcf and list of breast cancer mutations detected! I assume you want to focus on identifying mutations in BC gene unidentified samples. If you are looking for novel genes, then match the mutations you found in known BC genes to the samples and exclude these samples as cause identified and focus on the samples without a known cause. Prioritize the detected variants in those samples based on consequence (nonsense mutations first, missense second) utilize mutation prediction software to help you with these since some are harmless, and exclude common missense variants of frequencies more than 0.05 in genome databases (genome AD, 1000 genome project). Then when you have a shortlist, go through literature to identify functions of these genes or whether they were reported before in sporadic reports. Good luck.

For specified products like S294 antibody only from Abcam, I suggested contacting Cell signalling or Thermo Fischer technical support for the UK area. They are fast response using email.

Agree with Gordon here -- fixed-effect models are typically not adequate (see https://www.meta-analysis.com/downloads/M-a_f_e_v_r_e_sv.pdf)

There are a few vendors, but here is an option. https://sonovol.com/

Hello,

I have an interest in nanomedicine and am currently studying Breast Cancer (BC) so I would recommend starting with the following paper:

Di Wu, M. S., Xue, H. Y., & Wong, H. L. (2017). Nanomedicine applications in the treatment of breast cancer: current state of the art. International journal of nanomedicine, 12, 5879.

One of the most common medications used for BC treatment and probably the most effective so far is Doxorubicin. Perhaps this might be a better starting point before branching out.

I hope this helps!

Hello,

For aggressive cell lines, I recommend 100 000 to 200 000 cells to be injected subcutaneously to induce tumor in BALB/c mice.

Before trying to give a tentative answer, I would like to ask: What is your research question / are your research questions? And a bit nitpicky: Allowed by who?

My impression is that you have two quite distinct research questions:

- What is the effect on ovarian cancer of salpingo-oophorectomy in women who are BRCA2+ and have a history of breast cancer?

- What is the effect on breast cancer of mastectomy in women who are BRCA2+ without a history of breast cancer?

I expect that you will find no trials that address both questions at the same time, and even if they do, they will very likely report on the two questions separately.

Whether you say that you do one SLR or two does not seem to matter substantially, therefore I would say: call it what you think is best.

Doing one or two meta-analyses of course does make a substantial difference. I see no reason why you would want to put both those questions into one meta-analysis but maybe you do. E.g. is there any provider interested in the result of that one meta-analysis? (I can’t imagine that any patient has that interest, if only because no-one patient can have both a history of breast cancer and not have that.)

I wish you Mr Clarence Hu to be a doctor very soon . Best regards.

For Breast cancer induction mice are suitable because of mice are smaller in size and the induction period 3 to 4 month.

Hello Rachel Dassen. Well, you could convert your hand calculations into SPSS syntax. But I'm not sure that's what you're asking.

Which method of adjustment are you using, direct or indirect? Can you share the data (including the standard population info) with us?

Why are you opposed to using a regression model if it gives the correct results? HTH.

Qiagen has a RNA extraction kit specifically for tissue with a high lipid content (RNeasy Lipid Tissue Mini Kit) that might help maximize your RNA yield.

Thank you sir for your suggestion, My question is how to verify the SVM training model with testing data for FPGA implementation. I have stored testing data in BRAM.

Yes it will work fine, the detailed protocol can be obtained from this link. Best of Luck.

Try searching the imaging database at www.imagingQA.com at the link below :

These links may be of help

1)__ June 2021 paper in Nature / Nature Reviews - Genetics

Integrating single-cell and spatial transcriptomics to elucidate intercellular tissue dynamics

2)__ 10-X Genomics

A company and not hands on information…

but a decent introduction to the ideas

of spatial transcriptomics

3)__ July 2021 paper in Science

Embryo-scale, single-cell spatial transcriptomics

Access to full paper by one of three science literature groups

or purchase of the full paper

4)__ May 2021 paper in “Frontiers of Cell Biology”

Integrating Spatial Transcriptomics and Single-Cell RNA-seq Reveals the Gene Expression Profling of the Human Embryonic Liver

This is the full paper

I think there is a difference between BRCA1 and BRCA2. In general terms between 25-50% or even more. It may depend on the cancer, some are 33%. This one is quite high.

See these links:

In the LableMe tool, you can select a specific region and annotate it according to your class. But here you have a 200k dataset.

So what I suggest is, you can generate those text files automatically.

One of my research in a YOLO training dataset, I have used this technique to annotate multiple images.

Hello

The cells may be under stress. Did you follow a proper thawing protocol. The cells have to be washed in order to get rid of the freezing medium containing DMSO.

Sometimes, if the cells are not frozen in a proper manner or if there is variation in storage temperature then there could either be loss in cell viability or change in cell behaviour as in this case. Have you checked the cell viability after thawing?

I suggest you culture these cells in a smaller surface area like 6-well plate or T-25 flask so that the cells may come closer to each other and begin to adhere and grow.

Good Luck.

Hello Prof. Ramarao Malla

Immunogenicity is the ability to induce a humoral and/or cell-mediated adaptive immune response. The tumor neoantigens that are produced because of genomic instability in breast cancer cells, can be recognized by the immune system and induce T-cell responses and antitumor immunity. So, the burden of tumor mutations and the load of neo-epitopes are the two factors that are linked to response to immune checkpoint inhibitors.

Most of the breast tumors are immunologically silent, characterized by the presence of low mutation, neoantigen burden and few effector tumor infiltrating lymphocytes except for the three subtypes namely,

1) Triple negative breast tumors (TNBC) which are unique among breast cancer subtypes having a higher mutational load compared to other subtypes. In addition, higher levels of tumor-associated antigens suggests that immunotherapies are a promising treatment option.

2) High tumor infiltrating lymphocytes (TILs) and programmed cell death-ligand 1 (PD-L1) expression have been found in a considerable proportion of HER2+ breast cancer patients.

3) Estrogen receptor-negative and HER2 positive have also shown evidence of immunogenicity.

Best,

The viral cause of sporadic breast cancer (SBC) has been proposed based on an experimental mouse model of breast tumor induced by mouse mammary tumor virus (MMTV), Epstein-Barr virus (EBV), and human papillomavirus (HPV). While some studies have shown viral sequences of MMTV, HPV, and EBV in breast cancer cells, others have failed. Another study suggested that MMTV, HPV, and EBV have a potential role in the development of breast cancer and added more reasons to move forward in the search for a possible viral origin of breast cancer.

Kindly check the following RG link:

The Oncotype DX portfolio of breast, colon, and prostate cancer tests applies advanced genomic science to reveal the unique biology of a tumor in order to optimize cancer treatment decisions. In breast cancer, the Oncotype DX Breast Recurrence Score test is the only test that has been shown to predict the likelihood of chemotherapy benefit as well as recurrence in invasive breast cancer. Additionally, the Oncotype DX Breast DCIS Score test predicts the likelihood of recurrence in a pre-invasive form of breast cancer called DCIS. In prostate cancer, the Oncotype DX Genomic Prostate Score® test predicts disease aggressiveness and further clarifies the current and future risk of cancer prior to treatment intervention.

Hi Rafał Watrowski . Adity Pore was just asking why markers for the hypothetical EMT do not make sense in the 2 cell lines she is looking at.

I agree. The EMT is just a hand waving explanation of how epithelial cells, that are normally sedentary, suddenly become motile and invasive when they are cancerous.

good information regarding your question is available on....

Hello,

Depending on your protein's half life and siRNA efficiency, you don't need to deplete from serum. For instance, I manage to use my siRNA in 10% FBS and for a specific protein (which has a very short half life), after 48h my protein isn't detected by western blot. While others are still detectable but with a much lower expression level (knockdown effect). If this isn't applicable in your case, in my experience, certain cancer cell lines are adaptable, like the BT549. So you might consider also, changing your siRNA protocol to increase efficiency or the cell lines used, or a different adaptation protocol https://www.thermofisher.com/pt/en/home/references/protocols/cell-culture/serum-protocol/adaptation-of-cell-cultures-to-a-serum-free-medium.html