Author

I have a PhD in Molecular and Medical Genetics, and a Masters of Clinical Research. But in 2012 I quit my Stanford Postdoc to explore alternative careers. Now I am a Managing Editor at BitesizeBio.com and I love it.

I write this blog because I am passionate about academic reform.




13 comments:

Anonymous said...

Do you believe that immuno-specific antibodies(ex. Her2, etc.) specifically tag "recovered(tm)" targeted molecules/epitopes (microwave/embedded and/or fixed) in human tissue?

Technically denaturing already technically post mortem tissue and expecting specific binding without background and some non-specific binding seems even more of a stretch, don't you think?

Jen said...

There is always some nonspecific binding. But most antibodies are raised against short sections of proteins, therefore denaturing the proteins is usually not a problem, as a small epitope is not greatly affected by unfolding. There are also lots of tricks to ensure good signal-to-noise ratio, including appropriate fixing, unmasking and blocking. However,considering how your protein denatures is something to consider when designing antibodies, and something to especially keep in mind when trying to stain soluble and membrane-bound proteins.

Anonymous said...

What controls can you run?.. since biopsying normal tissue may not be an ethical option, right?
Also, I have been reading that Mastitis(bacterial) and Bartonella can all mimic Breast Cancer and each other histologically, in sonograms and radiography(mammograms). Does this include Her2 (etc. ) histostaining? This is reportedly rare, but is it possible that Oncologist, and Pathologists, do not look for bacterial infections or miss the mimicry? It also seems they may coexist. (References on request.)

Jen said...

Yes, cutting on normal, healthy people to obtain tissue would be unethical. Healthy samples will often come the perimeter of the cancer biopsy (some healthy tissue should always get excised along with tumor when performing lumpectomy or mastectomy). Also pathologists have lots of experience looking at normal tissue (breast of otherwise). This can be obtained a variety of ethical ways - cadavers, other medical waste (think breast reduction w/ permission). Obtaining normal samples is difficult but not impossible. Also many normal samples used for reference are very old (maybe before medical ethics were where they should be -- think Herieta Lacks) but well preserved histology sample can last almost indefinitely.

Yes there does seem to be some concern in the medical literature about mastitis sometimes masquerading as cancer.

http://www.sciencedirect.com/science/article/pii/S0960977603000328

http://www.ncbi.nlm.nih.gov/pubmed/22715267

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2687584/

etc.

It is and always has been a physicians greatest challenge to correctly identify a disease/condition. No test or battery of tests are perfect. Immunohistochemistry (IHC) is a long standing protocol with a good track record. However, IHC is finicky, needs good controls, and is vulnerable to inexperienced hands and improper interpretation. Also pathologists are people (often overworked, stress, distracted, etc) and judging by the literature Mastitis and breast cancer can be confused by them.

I am not an expert in breast cancer pathology. But from what I do know Her2 staining is used to ID a subpopulation of breast cancers (HER2 is overexpressed in 18-20% of invasive breast cancers). It helps the doctors decide what kind of treatments might work best based on the fact that a cancer is her2 positive (therefore her2 dependent). However, no her2 staining doesn't mean there is no cancer. There is not a global cancer marker (man, that would be so helpful). I do not know what battery of tests was done on all reported mastitis/cancer mix ups. I would have to read up on that.

From the few cases I looked it is appears the first identification is done with sonogram or mammogram - both notoriously unreliable for definitive diagnoses but a good place to start. Some patients then went on to further identification of cancer/infection with basic histology stains like H & E staining. (H & E staining uses non-specific dyes that mark the cells and membranes so they can be easily visualized by the pathologists.) It appears this is where the problem is. These cursory examinations may indicate erroneously cancer (which would undergo more advanced histology testing to ID sub type and stage, so likely not a problem for the patient), or more concerning cancer could be dismissed for mastitis -- I find this scenario unlikely as this type of mastitis is very rare and pathologists would likely "want to be on the safe side". From my brief lit survey it seems all patients received appropriate treatment, they just gave their pathologists a headache along the way.

Anonymous said...

Why not treat these breast masses with broad spectrum antibiotic before biopsy. Is there danger? Seems like the public often takes these broad spectrum antibiotics frequently with little proof of bacterial infection (frequently early viral or secondary combination), and few side effects (reported), so why not be sure the pathology does, or does not, respond to antibiotics. Seems cheaper, safer and more effective (layman's view..) than biopsy, mammography and sonogram, not to mention less invasive. This might also avoid biopsy and potential misdiagnosis and the initial characteristic trauma and fear of Chemo and Mastectomy.

(hope I didn't post this twice..)

Anonymous said...

Being on the safe side? Treating with Chemo before testing at least briefly with Antibiotics, Steroids, and other short term ‘less toxic’ therapies? Seems to many patients, I think you must agree, overly aggressive assuming all masses seem to be presumed to be some form of carcinoma. This seems weighted heavily in the direction of Cancer positive, even in a triple negative testing situation.
Why not! .. treat these breast masses with broad spectrum antibiotic before biopsy. Is there danger? Seems like a common precaution to pre-biopsy and surgery anyway, right? Seems like the public often takes these broad spectrum antibiotics frequently with little proof of bacterial infection (frequently, in early viral and/or secondary bacterial combination), and with few major side effects (reported), so why not be sure the pathology does, or does not, respond to antibiotics?? Seems cheaper, safer and potentially more effective (layman's view..) than ‘biopsy, mammography and sonogram’, not to mention less invasive. This might also avoid biopsy, and potential misdiagnosis, and the initial characteristic trauma and fear of Chemo and Mastectomy. But if not attempted, then the result might turn out that alternate diagnosis' (Masitis) might be considered “Rare”….(or seldom considered..and therefore un-seen)
Also, if two bacteria mimic cancer, then all three , Breast Cancer, Bacterial Mastitis, Bartonella ‘Mastitis’(…maybe all are Mastitis in reality) mimic each , how many other pathogens, viral, fungal and microbial, may also ‘mimic’ (this door has been opened, even if just apparently cracked).

Anonymous said...

Sorry about the double posting...first one of the last two did not show up until after I reviewed the repost.

Jen said...

I think the fear with blanket use of antibiotics is developing future resistant strains. This has the possibility of becoming a huge public health threat, while these mastitis/cancer misdiagnoses are very uncommon (low risk). I also assume most doctors do not want to wait a few weeks/months for steroids to work or not, before making a more definitive diagnoses with biopsies etc.
After all, every day is a day the cancer is growing.

Again I am not an expert on this topic. But there is always the chance for mistaken identity is diagnosing a patient. It is something physicians must keep in mind. But considering how rare it is, I am not sure there will be any protocol changes soon.

Anonymous said...

In general, 'the blanket use of antibiotics' is common practice. My daughter has been seen by this Oncologist and under her care for 4 weeks, reportedly reviewing files, re-acquiring histology and tissue for re-examination, Medicaid delays, etc. She's been through 5 biopsies (one setting)-no antibiotics, a recent catheter implant (pre-antibiotic/no post surgical anti biotic), and from my inquiries to Pathology and her advocate nurse, no consideration of localized Cystitis Bacterial involvement, but ….very little communications. It seems the Oncologist has been unavailable (out of town) for two weeks now..and advocate communications , vaguely suggest re-evaluation and retesting of tissue and initial Pathology results(2 locations-unexplained) is still…in progress. Also I seen no Endocrinology blood panels examined, but there has been little communication. After a CT (mod) scan the advocate suggested that there is “Cancer in the hip”..??
The more that I read, initially in alternate therapy sources, then in verify in PubMed sources, this mimicry and alternate diagnosis' count is now at my last count is at 4 (three bacterial-a new one "low trace Iodine levels"....). So the question becomes: are all of these other potential diagnoses (or root causes) "rare"??? or seldom examined and diagnosed.
Anyway let's face it, all diagnosis are built on years of theory and testing. These theories based on theoretical diagnostic techniques and statistics (that in my opinion may have included several significant groups, let’s just say, “riding buses 3 hour a day”…it wasn’t on the questionnaire…that will never be mentioned..). Is it …possible…that Cancer may not exist?! It may be only the theoretical manifestation of many, or any, "root causes"(biological failure, parasitic, biochemical, toxicity, anemia/chemical component deficiency,......). And unless you, or your 30 minute diagnosis (based on time spent in examination) Physician ...can find it, and insurance pays, you will be the victim of long or short term experimental chemo./radiation poisoning(this is accepted established!). The hope (no matter how slight) that "cancer cells", or whatever, dies first and faster assuming theoretically developed diagnostics have a 50% chance (if this is close..) of working....and 100% chance of side effects(that we will not discuss).....base on very complex Immuno-Histology (also fragile and highly theoretically based).

Anonymous said...

Answering my own question-Can anyone give me an example of "Her2 Staining of Bacteria"?: Dako Her2/Fish Staining Interpretation: "Ignore Bacterial DNA in Mast Cells and Macrophages (Highly Red Fluorescent cells that are clearly distinct from tumor cells with high Her2 Amplification)"
Did I get that right?(check link below) What does this mean ( ...to you)?

http://www.dako.com/29019_19feb10_her2_fish_pharmdx_interpretation_guide_gastric_cancer_fish.pdf

Anonymous said...

"POTENTIAL ADVERSE EFFECTS OF THE DEVICE ON HEALTH
HER2 FISH pharmDxTM Kit is intended for in vitro diagnostic use only. As with any in vitro diagnostic test, the potential risks are associated with incorrect result interpretations. A false positive test result would likely assign patients to receive a potentially ineffective therapy, possibly exposing the patient to serious side effects and, in rare cases, death. Alternatively, a false negative test result may exclude a patient who might benefit from therapy, potentially resulting in a poor outcome. Any potential adverse effects would be related to misuse of the device or interpretation error leading to potentially incorrect diagnosis and therapy selection.

"http://www.accessdata.fda.gov/cdrh_docs/pdf4/P040005S005b.pdf

Jen said...

You are right is assuming that cancer is not a blanket diagnoses. There are many root causes of cancer. There is more than one way for cells to "go wrong". That being said most of the methods for "curing cancer" whatever the origional cause are the same: chemo and surgery. If you both are unhappy about the communication you are receiving from your current physician I suggest you seek a second opinion on contact the hospital liaison to help facilitate communication -- you should feel comfortable with the doctors diagnosis. I do not have experience myself with the Her2 staining, I also do not know what kit or antibody source your daughter's hospital is using to diagnose. the background (erroneous) staining can vary greatly depending on the exact protocol. I do not know it if the mast cells are expected to autofluoresce with that kit or if it is a staining artifact. Again I have to not used that kit before. That being said the mast cells look very different and if the Drs excluded them (as the kit suggests) that is the conservative way to diagnose her2 positive breast cells.

As for the second post that looks like normal boilerplate "please don's sue us" language.

Anonymous said...

Medicaide patients probably can not sue...(don't need a comment..) ..This is..her second doctor. Medicaide and something else(?) changed this.
Guess I'll try to get away from the ethics issues...all humans seem to struggle with ethics.
Technically, I am just questioning Specificity of Diagnosis...and technology. I never believed in single specific answers, only "trial and failure", then "re-trial and different failure", and then “ pick the least destructive failure". (Kind of like "House"). Time and total destruction are always the limits of R&D/and failure /root cause analysis.
When I assisted Med. School labs, worked with Bio-R&D folks, and helped create the data(EM). I was very concerned that they (all) rarely understood the complexity and limits of the instrumentation they used. I was once criticized (bio-technically monitored) for simple ionicity(ion concentration) and osmolarity and some component buffer level issues that were critical to the “deep-etch” experiment that I was expected to complete. My co-workers and team leaders were sure I should have known the procedures, but it turned out that I was working on the edge of the capability of these instruments (freezing point depression and more standard lab instruments)....I then I discovered I was 'alone'...no one had experienced or understood this technology. I was surrounded by people with degrees and training much higher than mine, and their assumptions and specialized instructions were, I soon recognized, were text book generalities, not experience. I have stumbled into these "gaps" many times since then in many other technologies. Now I know how to carefully recognize and work with these technical voids..very cautiously and document, document, document,..find the sources of the compromises...find different approaches...to generally a "cloud of confidence".
In freeze fracture (cryo-vitrification dependent), in fixation, especially staining(!!), in polymer structures,...etc. some of the highest level of misinterpretation and simplest solutions seem to be 3-dimensional interpretation(or the lack of it) and the second in "Diagnostic Specificity"(or lack of it). Biological dynamics have always seemed to me the primary source of a huge area of misunderstanding and misinterpretation.
Have you ever heard or read the Single Mitochondria (or bacteria) Theory? From an interpretation using Freeze-fracture (artifact), it appears that organelles are simply "involutions" and the organelles are exterior, not interior. The Inner Membrane Particle may only be hydrophilic discontinuities (not protein or glycoprotein or compex-phospholipid or..?..). I have never seen this in the text-books (Med), only in peer reviewed literature. The popular misleading simplicities always take the pages of our education.
Do stains actually chemically stain, or fix, or destroy, or get "trapped"? (all!) Does Medical Imaging Technology define anything except density function?
("and that's all I haveto say ab-ouy Tha-at." Q: Forest