Intersection of Oncologic and Molecular Pathology
February 18, 2022Information
Feb. 17, 2022
Yale Pathology Grand Rounds
Joanna Gibson, MD
ID7469
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- 00:00Well. While people are still
- 00:04logging in, we have 60, so I'll
- 00:08get started with the introduction.
- 00:13Most people don't need an introduction to
- 00:17Doctor Gibson, Doctor Gibson, but so my
- 00:20introduction is going to be very brief.
- 00:24Dr Gibson did her bachelor's in science
- 00:28from University of Minnesota and then
- 00:32went on to do MD PhD at the Mayo Clinic's
- 00:37School of Medicine. Following that,
- 00:40she went to Brigham and women.
- 00:44For a pathology residency,
- 00:46and she must have liked the northeast
- 00:51so much that she decided to pursue
- 00:55further career in the Northeast,
- 00:58finishing up with a chief residency at
- 01:01Brigham and Women's and then a GI Fellowship.
- 01:05She followed this with a brief stint
- 01:08back at Mayo Clinic and came right
- 01:11back and joined our department.
- 01:14In 2011, as assistant professor and
- 01:18now Joanna Gibson is an associate
- 01:22professor in GI pathology.
- 01:25She serves on many committees and is
- 01:29currently the director of Quality
- 01:32and Patient Safety.
- 01:34In Joanne's practice,
- 01:36she combines molecular pathology
- 01:39and GI pathology,
- 01:41and today Doctor Gibson will
- 01:43share her insights. Indu.
- 01:46Oncology and molecular pathology.
- 01:51A brief housekeeping notice that from today.
- 01:55Unfortunately,
- 01:56there has been a change to how
- 02:00CMA credit is given when you text
- 02:04your CMA credit number.
- 02:06If your CMA profile is up to date
- 02:10with regards to disclosure of
- 02:13conflicts of interest and other stuff,
- 02:17you would get CMA credit.
- 02:20Otherwise,
- 02:20you may.
- 02:22Get a message that your profile is
- 02:26not up to date and Susanna has now
- 02:30found this out just today and she sent
- 02:33an email to the entire department.
- 02:36So it's a simple fix.
- 02:39Just update your CMA profile.
- 02:42With that, I'll let Joanna take it away.
- 02:46Thank you Manju. Share my screen.
- 02:54Go to presentation mode. Hopefully you
- 02:56guys can see that presentation mode.
- 03:01Yes, great. I'm going to try
- 03:03to use this laser pointer.
- 03:05See if that works for highlighting things.
- 03:08So Andrew, thank you so much for
- 03:11the introduction and thank you so
- 03:13much for the opportunity to come
- 03:14and give Brian Rounds and in our
- 03:17own department it's definitely a
- 03:18privilege to be able to do that.
- 03:21So I just want to come back to my early
- 03:24education and pathology and sort of
- 03:27explain a few things that sort of.
- 03:30Have led to where I am today so my
- 03:33interested oncology started early.
- 03:36In my, you know when I got to the Mayo
- 03:38Clinic for my for my MD PhD training.
- 03:42You know, I started to get
- 03:44interested in cancer biology,
- 03:45and I succinctly remember a lecture
- 03:48that Doctor Brookhart gave when he was
- 03:50there at that time, and I I really,
- 03:52he was my first example of sort of,
- 03:54you know, how do you study cancer?
- 03:56How do you look at it?
- 03:57I think it triggered my interest
- 04:00in pathology and once I got to
- 04:03residency and into my fellowship,
- 04:05I started to sort of submit my interest
- 04:08specifically more in GI cancers
- 04:10and specifically colorectal cancer.
- 04:12And so yes,
- 04:13I kind of went back and forth the
- 04:15East and West Coast and just going
- 04:18to do one thing here and move now,
- 04:21I can't do it just one second here guys.
- 04:28The zoom window is interfering with my
- 04:31view of the slides and it was I didn't
- 04:34move it out of the way. And so I.
- 04:41So when I arrived at Yale,
- 04:42I already had a very strong
- 04:45interest in oncology and cancer,
- 04:48specifically colorectal cancer.
- 04:50And you know, when I got into
- 04:51the Yale practice, that's sort of
- 04:53where I focused my efforts and so.
- 04:56Hopefully throughout this talk you'll
- 04:58get to see how that intersection.
- 05:01Of oncology pathology molecular pathology
- 05:04occurred for one GI pathologists practice
- 05:07myself and specifically how does the
- 05:11intersection sort of lead to patient?
- 05:15Management changes and and you
- 05:17know how we impact patient care.
- 05:20So conceptually, this is how I'm going
- 05:22to sort of present my grand rounds.
- 05:25I'm going to use patient examples
- 05:27to highlight different biomarkers,
- 05:30different technologies,
- 05:31and different effects on patient impact.
- 05:35So hopefully throughout this entire talk,
- 05:36they'll be sort of a common theme of
- 05:39that progression of of data sharing.
- 05:43Alright,
- 05:43so starting with patient number one
- 05:46this was a 45 year old man who had
- 05:48his first screening colonoscopy and
- 05:49was diagnosed with colon cancer that
- 05:52you can see here on the endoscopic
- 05:54picture and on the Histology image,
- 05:58and so I'll invite the residents to
- 06:02use the chat if they want to and what
- 06:06molecular tests should be ordered and why.
- 06:11Open the check my other screen.
- 06:18And.
- 06:22So the answer should be MSI
- 06:25testing exactly excellent.
- 06:32Somehow something is getting stuck
- 06:35in my PowerPoint, I apologize.
- 06:39I have to quit one more time.
- 06:41There we go alright? So.
- 06:47Colon cancer remains one of
- 06:50the most common cancers.
- 06:51That's third common in both
- 06:53men and women after prostate,
- 06:55in Latin or breast and lung cancers,
- 06:57and it also remains a.
- 07:00You know high high contributor to
- 07:03cancer deaths in both men and women,
- 07:06and so it still remains a major problem in.
- 07:11In the United States and worldwide,
- 07:13and I wanted to make the patient
- 07:15the age at 45 because recent
- 07:17reports have shown that there's a
- 07:19rising incident saying patients,
- 07:21and I I really wanted to bring
- 07:23this into this presentation
- 07:24to just make everybody aware.
- 07:26And although we have done a
- 07:29really good job in decreasing
- 07:31cancer rates in older populations,
- 07:33we it had been noted that the younger
- 07:37patients are having increasing rates and.
- 07:41And the problem is,
- 07:43is that the young populations are not,
- 07:45you know,
- 07:45not being screened as screening age
- 07:48was greater than 50 for many years,
- 07:50and most recently because of this data,
- 07:52the American Cancer Society has
- 07:54recommended that people at age 45
- 07:57start undergo regular screening
- 07:58for colorectal cancer.
- 08:00And this is true for patients
- 08:01with average risk.
- 08:02Obviously,
- 08:02if there's any other risk factors that
- 08:05age of of screening might might also change.
- 08:09And so diagnosis in colorectal
- 08:12cancer is something that we do
- 08:14every day as GI pathologists.
- 08:16Here I have an example of a
- 08:18malignant polyp that shows a little
- 08:21bit of residual benign adenoma on
- 08:23the side of this of this tumor.
- 08:26But bulk of this small,
- 08:28malignant polyp is composed
- 08:30of invasive adenocarcinoma,
- 08:31so we recognize the Mulligan glands,
- 08:34but they're atypia irregularity,
- 08:36and it doesn't plastic stroma.
- 08:39And when I see a slide of cancer,
- 08:42I automatically just my mind
- 08:45comes to the molecular pathways
- 08:47of colorectal carcinoma and.
- 08:50What's exciting about colorectal personal.
- 08:52It's it's one of the first examples
- 08:56of a carcinogenesis pathway of of
- 08:59showing how cancer can go from benign.
- 09:02Lesions to invasive lesions that impact
- 09:06patient health and patient mortality,
- 09:10and there are multiple pathways
- 09:12that colorectal cancer can form,
- 09:14and so when I'm sitting and looking
- 09:16at these slides of colorectal cancer,
- 09:19I'm always thinking is this a,
- 09:21you know, conventional pathways.
- 09:22This is the rate of pathway and for the
- 09:26purpose of MSI testing of why that's there,
- 09:28it's because we do have a familial
- 09:30pathway of colorectal cancer.
- 09:31And there's two main.
- 09:33Pathways,
- 09:33Faps and Lynch Syndrome FAP is
- 09:35generally fairly easy to diagnose
- 09:37once you get to colonoscopy.
- 09:39This is a phenotype that is quite dramatic.
- 09:43There's hundreds and hundreds of
- 09:45turbulent moments within the colon,
- 09:47and so when patients get their
- 09:50first colonoscopy,
- 09:51the diagnosis can be made relatively easily.
- 09:53Lynch syndrome, on the other hand,
- 09:55does not have a polyposis.
- 09:56The old name for Lynch syndrome was
- 09:59non polyposis colorectal carcinoma.
- 10:02And. And so this.
- 10:08So,
- 10:08so being able to recognize
- 10:09Lynch syndrome is an
- 10:10important component to try.
- 10:12You know, to try to identify whether
- 10:14the patients that we are seeing
- 10:16have a genetic predisposition,
- 10:17which then will impact not just
- 10:20that patient but also their family.
- 10:22And Lynch syndrome is the most common
- 10:25form of heritable colorectal cancer.
- 10:28Probably accounts up to two to
- 10:303% of all colorectal cancer.
- 10:32It has an autosomal dominant inheritance
- 10:34pattern and most importantly,
- 10:36it is associated with cancers
- 10:37outside of the GI tract as well,
- 10:39primarily in the mutual cancer,
- 10:41but various other ones to a lesser degree.
- 10:44And for many years,
- 10:47diagnostic criteria or based on
- 10:49the Amsterdam features which.
- 10:51Which really mostly looked at family
- 10:53history to be able to make a diagnosis
- 10:56at this particular syndrome and what
- 10:58happened in the 90s and into the 2000s,
- 11:01which is kind of when I was getting my PhD.
- 11:04Some of you know,
- 11:06some really important discoveries were made.
- 11:08One was that Lynch syndrome.
- 11:11Was.
- 11:13Was discovered to be related
- 11:16to microsatellite instability
- 11:18in the tumor cells and the.
- 11:21Set of four mismatch repair proteins
- 11:24were identified as the genetic cause of
- 11:28large syndrome and in at least one study,
- 11:31the most common mutation that's found
- 11:33in Lindstrom is MSH 2 and MLH 1 being
- 11:37a close second common with the other
- 11:39two being less frequent and just to
- 11:42remind everybody what are microsatellites.
- 11:44Microsatellites are
- 11:45repetitive regions of DNA.
- 11:48They can be found through they're
- 11:49found throughout the genome,
- 11:51including.
- 11:51Within exons of of important genes
- 11:55and they are particularly sensitive
- 11:57to replication errors to mismatches.
- 12:00So here you can see a mismatch occurred in
- 12:04this particular area and these proteins.
- 12:08These mismatch repair proteins repair
- 12:10that mismatch and if they are absent.
- 12:13If these proteins are not able to function,
- 12:15this mismatch is not repaired and you
- 12:17get you end up with variably sized
- 12:20alleles at that particular Microsoft like.
- 12:22So focus which can then be seen an
- 12:26old-fashioned gels which you know don't
- 12:29don't get done really anymore that much.
- 12:32So how does that you know
- 12:35really occur in more detail?
- 12:37So basically the mismatch is
- 12:40originally recognized by a
- 12:42heterodimer of MSH 2 and MSH 6.
- 12:45Which then recruits another
- 12:46heterodimer of MLH one and PMS two,
- 12:49and these heterodimer
- 12:50formations are really important.
- 12:51And once once this mismatch is recognized,
- 12:55other proteins get recruited to the
- 12:57site of this particular DNA mismatch,
- 12:59which then excised the region of the
- 13:02DNA that is involved and that gets re.
- 13:07Be synthesized and the heterodimers can be.
- 13:14Can be.
- 13:18And the reason that the heterodimers
- 13:21are important is because when you have
- 13:24a missing part of the heterodimers.
- 13:26So let's say there's a mutation and one
- 13:29of the genes that forms a heterodimer.
- 13:31The heterodimer is unstable and both
- 13:34proteins end up getting degraded.
- 13:37So if you have like a truncating
- 13:39mutation or something like that of 1,
- 13:41the other protein becomes unstable as well,
- 13:44and so we can see this.
- 13:46In the IHC that we do every day for
- 13:50four MMR proteins that we see the
- 13:52predominant pattern that we see
- 13:54is the paired loss of expression,
- 13:56and that's because of this biologic.
- 14:01Process of of the heterodimers
- 14:04being unstable when one is mutated.
- 14:07And conversely,
- 14:08when we see paired loss of expression,
- 14:10you know the other.
- 14:11The other header dimers usually
- 14:12shows preserved expression,
- 14:14although there are rare examples
- 14:15where all four might be missing.
- 14:18And so how does colorectal cancer
- 14:20develop and Lynch syndrome?
- 14:21There the model is an accelerated
- 14:25carcinogenesis model that adheres
- 14:27to nuisance hypothesis for the first
- 14:29hit is the germline mutation in one
- 14:32of the four at the margins and the
- 14:34second hit is a acquired somatic
- 14:37mutation of the paired MMR gene,
- 14:40usually within a adenoma that forms
- 14:43sporadically within within these
- 14:45patients and the thought is that.
- 14:47Sporadic I don't know.
- 14:49Must have formed an Ellis in a
- 14:51Lynch syndrome background.
- 14:53Will progress the cancer much
- 14:55faster than they would in a non
- 14:57Lynch syndrome patient.
- 15:01And here you can see an example of
- 15:02an adenoma that has lost so that
- 15:04knowledge one and PMS 2 not all of.
- 15:06Not all adenomas will show that in
- 15:08Lynch syndrome it's partly depends on
- 15:10the extent of you know of the pathway.
- 15:13That's that's progressed,
- 15:14at which time we actually see the biopsy.
- 15:18And so the current guidelines have been
- 15:22refined over the last decade or so,
- 15:25and now there's, you know,
- 15:26very strong recommendation.
- 15:28That there should be universal
- 15:30screening of all colorectal carcinomas
- 15:33to maximize the ability to identify
- 15:36patients with lips syndrome.
- 15:38And you know, and the mutual carcinomas
- 15:42are part of this recommendation.
- 15:44And I'm, you know,
- 15:44I'm going to leave it to others
- 15:46to talk about.
- 15:46End of mutual adenocarcinoma and
- 15:49and those you know.
- 15:52Special features that are
- 15:54associated with that tumor type.
- 15:58But more recently,
- 16:00the guidelines have also expanded
- 16:02the tumor types that should be
- 16:05included in that screening process,
- 16:07and that those tumors you know.
- 16:11Consider doing screening for
- 16:13other GI tractors. Small bowel,
- 16:16gastric pancreas, and you know, etc.
- 16:18And another important aspect of
- 16:19the new recommendations is that an
- 16:22infrastructure needs to be in place
- 16:24to handle the screening results.
- 16:28And the guidelines are actually interesting
- 16:31because they don't really come down on
- 16:33any particular method of screening.
- 16:36The two methods that are discussed in
- 16:38those guidelines are immunohistochemistry
- 16:40and the preliminary chain
- 16:42reaction or PCR, and you know.
- 16:46So both are accepted methods of
- 16:49screening and both have their own.
- 16:52Pluses and minuses in terms of what
- 16:55information and how sensitive they
- 16:57are for for capturing the patients.
- 17:00Immunohistochemistry is really the
- 17:02preferred initial method in practice,
- 17:05so most labs have ability to do
- 17:09immunostains that so this is an expensive
- 17:11and it's widely available and it's
- 17:13fairly easy to express to assess for
- 17:15the expression of them are proteins the
- 17:18turn around time is also very quick,
- 17:20and and as we'll see the pattern of MMR loss.
- 17:24And also suggest Lynch syndrome.
- 17:27And.
- 17:31And guide any additional testing
- 17:33manshu I see your question.
- 17:37So I do not know specific associations
- 17:41with head and neck tumors.
- 17:44With Lynch syndrome specifically,
- 17:46but if you do, you know I'm.
- 17:49I'm sure there have been reports,
- 17:51but I'm not aware of any,
- 17:52and if anybody else knows,
- 17:54feel free to chime in.
- 17:59The PCR method is used mostly at
- 18:01least in the realm of colorectal
- 18:04cancer as a confirmatory method,
- 18:06complementary method.
- 18:07It's not the primary method of screening,
- 18:09and it does require a
- 18:13molecular laboratory ability,
- 18:14so this limits its its availability,
- 18:18although these days.
- 18:21Most academic centers have a molecular
- 18:23laboratory where this can be done
- 18:25the turn around time is a little bit
- 18:26longer because there is a step of
- 18:28DNA extraction that needs to be done
- 18:30and and for a long time people sort
- 18:32of argued in literature about which
- 18:34microsatellite markers are the best, etc.
- 18:36And you know, I'm not going to
- 18:38go into those kind of details,
- 18:41but usually at least five microsatellite
- 18:44markers are tested to look for instability.
- 18:47And, importantly,
- 18:48the PCR reaction will not be able
- 18:52to distinguish inherited forms
- 18:54and sporadic forms of MSI cancer.
- 18:56And we'll look at that a little bit more.
- 18:58So here's result.
- 18:58Number one.
- 18:59Here we have an add no carcinoma that
- 19:02shows clearly shows loss of MSH 6 at MSH.
- 19:062 in the tumor with preservation
- 19:07of MLH one and PMS 2.
- 19:09One important aspect of interpreting
- 19:13MMR stains is that you should
- 19:16look for intervening benign cells
- 19:18that have preserved staining.
- 19:21So in the MSH 16 that's a little bit faint,
- 19:25but you can see that there's some brown
- 19:27staining of the intervening stromal cells,
- 19:29mostly lymphocytes it looks like,
- 19:31and in the MSH 2 stain that
- 19:32is a little bit stronger,
- 19:34so there is some variability in in these.
- 19:38And and how you know what this
- 19:40looks like with results?
- 19:41And So what should happen next?
- 19:45Anybody have an idea?
- 19:48I'll give residents half a
- 19:50second to think about it.
- 19:57So the next step is well, so you can look
- 20:02for any algorithms that there's many,
- 20:05many algorithms that exist to help you
- 20:07figure out what to do with those results.
- 20:10So with the loss of MSH 2 and
- 20:13MSH 6 or isolated loss of PMS 2.
- 20:17The patients should be referred
- 20:18to cancer genetics.
- 20:20No additional testing is needed.
- 20:21They should just go to cancer,
- 20:22genetics and cancer.
- 20:23Genetics will take care of the rest.
- 20:25We don't need to worry about it.
- 20:28And we are really lucky at
- 20:31Yale because we do have that
- 20:35infrastructure in place that.
- 20:40That sorry, somebody is direct
- 20:43messaging me for the CMU code.
- 20:46That should be, uh, that's already
- 20:48been sent a couple of times.
- 20:50Yeah, just just ignore. Ignore, yes.
- 20:55And so we do have an infrastructure in place.
- 20:59We do have a cancer genetics
- 21:00and prevention program.
- 21:01They're located at on the SRC campus,
- 21:04and the one of the directors of the
- 21:06program is Shabbir Lor, who's endoscopist.
- 21:10And and so, like I said,
- 21:13we're lucky that we have this infrastructure,
- 21:15and they've actually at Yale.
- 21:18This infrastructure has actually
- 21:19changed over over the years.
- 21:21Initially, you know, we had universal
- 21:24testing for colorectal cancer for a
- 21:26number of years now and initially.
- 21:31But it was dependent on the provider,
- 21:34you know.
- 21:35So we see the biopsy of the cancer.
- 21:37We do the immunostains.
- 21:39We write a report of that,
- 21:41and it goes back to the endoscopist to have,
- 21:44you know,
- 21:45to have that result and then it
- 21:47depended on that endoscopist to be
- 21:49able to refer the patient to genetics.
- 21:51Well, this this genetics clinic
- 21:54decided you know what?
- 21:56Screw that.
- 21:56Let's let's see if we can get to
- 21:59this data a little bit more a
- 22:01little bit faster and so they've.
- 22:03They've you know,
- 22:05created some automated review at
- 22:08First pathologist review and now
- 22:11an automated review for colorectal
- 22:13cancer and and it's turned out
- 22:16that with this strategy where they
- 22:18get an automated report of all the
- 22:21patients that meet certain criteria
- 22:23with the results they've been able
- 22:26to identify eleven additional Lynch
- 22:28syndrome patients in in this time frame.
- 22:31And it it.
- 22:32Seems to be a cost effective way
- 22:34of doing this material and this
- 22:36this data had been presented at
- 22:39a couple of different meetings.
- 22:42Over the last couple of years,
- 22:44and so we you know,
- 22:46we again all we need to worry as
- 22:48well exists is that we report the
- 22:51results and those results will be
- 22:54automatically sent over to the
- 22:56genetics clinic for them to be
- 22:58able to reach out to the patient
- 23:00and to the provider of the patient
- 23:02to create that genetic consult.
- 23:05For confirmation of diagnosis.
- 23:09And MRI is usually pretty
- 23:13straightforward to interpret.
- 23:15There's you know it's really just as
- 23:17the is there standing as they're not,
- 23:19but there are a couple of cautious
- 23:23caveats that should be kept in mind.
- 23:25If you have a very small amount of tumor,
- 23:28you know,
- 23:29be cognizant that limited tumor samples.
- 23:33May have, you know,
- 23:35maybe under you know,
- 23:37maybe over called for absence of tumor
- 23:39staining if you're only looking at a
- 23:41a few glance of tumor and also some
- 23:44unusual patterns have been reported.
- 23:46Some of those are things like
- 23:49this dot like powder.
- 23:50Majority of these are associated
- 23:52with lots of protein.
- 23:53It's an abnormal expression pattern
- 23:55and so if if you're ever in doubt
- 23:58you can always order the PCR to
- 24:00confirm that there's presence of
- 24:02microsatellite stability and false
- 24:04negative results are pretty rare.
- 24:07They will occur in less than 10% of.
- 24:10Of patients and that can occur because
- 24:13depending on the mutation type,
- 24:15it may not be.
- 24:16Activity can still be preserved
- 24:17even though there is actual
- 24:18dysfunction of the protein,
- 24:19so it it can happen.
- 24:21It's a biological phenomenon that's
- 24:23quite possible and more recently with
- 24:26one of our residents not allowed.
- 24:28Smote. Oh, I have done a small study to
- 24:32look at our MMR staining here at Yale,
- 24:36and we looked at 150 patients who
- 24:39had two or more MMR IHC results.
- 24:42And it turns out that most of those
- 24:44MMR results are quite reproducible,
- 24:46and so it's a robust test,
- 24:48and we did find this coordinate MRI
- 24:50HC patterns and 6% of patients and.
- 24:56And. Those 6% primarily were
- 25:01independent primary tumor,
- 25:03so if a patient had a primary of,
- 25:05you know colon and a primary,
- 25:07you know of breast, they might show
- 25:09different patterns of IHC because they
- 25:12will arise through different mechanisms.
- 25:14And then I have a question from Doctor Robert
- 25:17about utility of them are in adenomas.
- 25:21And so yes, adenomas can show loss
- 25:26of of MMR proteins, but not always.
- 25:29It's, you know, if you find loss,
- 25:32that's great,
- 25:32and you can certainly use that
- 25:36information to suggest genetic counseling.
- 25:39But if you find preserved IHC,
- 25:42it does not rule out the
- 25:44possibility of Lynch syndrome.
- 25:46In that case,
- 25:47I don't have a slide specifically
- 25:48addressing this question.
- 25:52Alright, so here is another result,
- 25:54so this is another possible outcome.
- 25:56Here we have a mucinous adenocarcinoma.
- 26:00You can see a lot of you know mucin
- 26:02production with the malignant lens
- 26:04here and we see loss of MLH one and
- 26:06PMS two and again we always want
- 26:08to look for positive staining in
- 26:11the intervening normal cells that
- 26:13are present within the around.
- 26:15The tumor within the tumor.
- 26:17And we have preservation of MSH 2 and MSH 6.
- 26:19So what's the?
- 26:21Next step here anybody.
- 26:29So I'll just move on to that,
- 26:31let's see. There you go.
- 26:34So the answer is that we should
- 26:36go to MLH 1 methylation and the
- 26:38reason why we need to do that is
- 26:40because we need to distinguish.
- 26:42Tumors that occur in the setting of Lynch
- 26:44syndrome from those that occur sporadically.
- 26:46So here is our algorithm and
- 26:48so now we have lots of MLH,
- 26:50one with or without loss of PMS
- 26:53two this should trigger.
- 26:56Ordering MLH 1 metalation PCR to
- 27:00determine what happens and the MLH 1
- 27:03methylation specific PCR is performed
- 27:05in our Yale Molecular Diagnostics Lab,
- 27:08so it's pretty easy to to do that
- 27:12ordering and depending on what the MLH
- 27:161 methylation results show you would
- 27:21you would refer the patient to genetics,
- 27:24so if no methylation is seen.
- 27:27Of MLH one, then the patient should
- 27:29be referred to cancer genetics,
- 27:32and so that's the reason.
- 27:33Why is because there's two pathways
- 27:35to MSI and colorectal cancer,
- 27:37and they're actually both quite different.
- 27:38So we've talked at length about Lynch
- 27:41syndrome and I wish I see your answer.
- 27:44I I, you know, I, I didn't.
- 27:47I didn't see it fast enough to read
- 27:49it as I started to explain the answer.
- 27:52But you're absolutely correct,
- 27:54methylation.
- 27:55So the Lynch syndrome we've already
- 27:57talked about.
- 27:57We talked about how patients have
- 28:00germline mutations and they get a
- 28:02second hit in their adenoma which can
- 28:05then lead to deficient mismatch repair.
- 28:08Ultimately,
- 28:09microsatellite stability and
- 28:10with microsatellite stability
- 28:12come secondary mutations and a
- 28:14variety of coding microsatellites.
- 28:16And it can lead to and all
- 28:18of that leads to cancer.
- 28:20Sporadic MSI cancers are quite different,
- 28:24although the end result is very similar
- 28:27meaning that they do end up with
- 28:29the same deficient mismatch repair.
- 28:31But the mechanism and the process is
- 28:34very different and so MSI high sporadic.
- 28:39Cancers occur through the serrated pathway
- 28:42of carcinogenesis and in this pathway,
- 28:45sessile strated polyps are
- 28:47thoughts develop a intermediate,
- 28:50dysplastic steps.
- 28:51Most SSPS will.
- 28:53This will have beer after 600 imitation,
- 28:57so these tumors also very commonly
- 29:00have fee 600 mutations and then
- 29:03what happens and you know.
- 29:05It's it's really unclear how
- 29:07this starts or why you know what
- 29:09is it within an SSP that allows
- 29:12for this mechanism to occur.
- 29:14But what is that to happen is
- 29:16that the MLH 1 gene is silenced
- 29:19in an epigenetic fashion through
- 29:22methylation of the promoter of MLH one.
- 29:24So here's all of these CPG islands
- 29:26that end up getting methylated,
- 29:28and once it is methylated the chromatin
- 29:32closes up and is inaccessible to being.
- 29:36Transcribed and the protein
- 29:38can no longer be expressed.
- 29:40So virtually all cases of sporadic.
- 29:47MSI high cancers will have
- 29:49MLH 1 promoter methylation,
- 29:51which we can test for and the result
- 29:55is that patients get MSI high cancers.
- 29:59These tend to be poorly differentiated
- 30:02or mucinous in nature.
- 30:04They also have other associations such as
- 30:06more commonly being found on the right side,
- 30:08more commonly being found in older
- 30:11patients and female patients.
- 30:13They do tend to have a good prognosis and
- 30:15there are some specific. Therapeutic?
- 30:20Options for these patients. And so.
- 30:26Going back to our paradigm,
- 30:29this is where we would determine
- 30:31if if a patient needed referral
- 30:33to genetics or if they have a
- 30:35sporadic form of MSI high cancer
- 30:37when it comes to loss of MLH 1.
- 30:47And so moving out patient two patient
- 30:50two is a 50 year old woman she had.
- 30:53She was diagnosed with a right sided add no
- 30:56carcinoma and we already had testing done.
- 30:59She had MLH one and PMS two loss.
- 31:02So you can see those there.
- 31:04She was positive for MLH 1 methylation.
- 31:08So we think it's sporadic.
- 31:11It's a sporadic I'm.
- 31:12It's like I can't, Sir,
- 31:13but the note was that she had
- 31:16greater than 50 polyps in her colon.
- 31:19So what is a possible diagnosis and
- 31:21the hint is that she ended up with a.
- 31:26Total colectomy and majority of
- 31:28her polyps versus ulcerated polyps.
- 31:33And if any of the residents
- 31:36have an idea of. Of a diagnosis.
- 31:45Alright, so the possible diagnosis is
- 31:47that the patient has severe polyposis
- 31:49syndrome and this continues to be an
- 31:52underrecognized colorectal predisposition
- 31:54polyposis syndrome that is specifically
- 31:57associated with MSI high MLH one loss
- 32:01and MLH 1 methylated carcinomas, and.
- 32:07Men and women tend to get this equally.
- 32:10This can be seen at any age.
- 32:12And it's usually diagnosed unexpectedly
- 32:15at screening colonoscopy or or at.
- 32:18Or colectomy, there's two main variants.
- 32:22Type one and Type 2,
- 32:23based on sort of the location and
- 32:25number of polyps that are found in
- 32:27and these sort of correlate with
- 32:29The Who criteria for SPS diagnosis,
- 32:34so criterion one is, you know,
- 32:36more than five strated polyps proximal
- 32:38to the ****** and they have to be,
- 32:39you know, greater than 5 millimeters and
- 32:41two of them have to be greater than one.
- 32:43I mean that gets a little bit wordy.
- 32:45Where's the Criterion 2 is,
- 32:46you know greater than.
- 32:4923 polyps anywhere in the colon with no
- 32:52particular size criteria and you know,
- 32:55even though this is a fairly
- 32:58distinct polyposis syndrome,
- 33:00genetics are not understood, not known.
- 33:05Have not been, you know,
- 33:06specific Gene has not been discovered.
- 33:08That sort of explains
- 33:10majority of these cases,
- 33:11although some some have been proposed.
- 33:14At the Scopic Lee,
- 33:15these patients just have multiple polyps
- 33:17and they tend to have this characteristic
- 33:19mucus cap so so they can be recognized,
- 33:21and the scopic Lee somewhat.
- 33:23If there is ability to do
- 33:25confocal laser endoscopy,
- 33:26which you know most places
- 33:28don't have that ability,
- 33:29there are some unique features
- 33:32that can be that can be detected,
- 33:35such as these thin branching.
- 33:37***** and dystrophic goblet cells.
- 33:40When you look at the specimens grossly again,
- 33:42there's no distinctive features.
- 33:43The polyps tend to be sessile,
- 33:45and you know,
- 33:46so if you notice one of these types of
- 33:48phenomena in the in the colon cancers
- 33:51that you gross sampling of multiple
- 33:53polyps is crucial for the deduction of SPS,
- 33:56and the reason why is,
- 33:57if you have a partial colectomy and a
- 33:59patient has serrated polyposis syndrome,
- 34:01it might be that they are,
- 34:03you know, continues to be a high
- 34:04risk for developing cancer,
- 34:06and their remaining colon.
- 34:07That they have and in one small
- 34:10study that had done a few years ago,
- 34:13we found in a cohort of 22 patients who had
- 34:16colectomy and were found to have polyposis,
- 34:19we actually found SPS as the cause of
- 34:22the polyposis in about 1/4 of them.
- 34:25And furthermore,
- 34:26in a separate study,
- 34:28we looked at a population of
- 34:31over 2000 patients who had at
- 34:34least one pseudopolyps diognosed.
- 34:36And we found that one point 4% or 32
- 34:40patients met criteria for serrated
- 34:43polyps syndrome and these patients
- 34:46had a variety of polyp types.
- 34:49Many of them had advanced neoplastic
- 34:52features, so they either had,
- 34:53you know,
- 34:54dysplasia within their serrated polyp,
- 34:56or frank invasive carcinoma and
- 34:58what's interesting is that these
- 35:01carcinomas actually had a variety
- 35:03of augmentations within them.
- 35:04So even though the prevalent thought is
- 35:07that these. Cancers all lead to you know,
- 35:09one type of MSI high tumor
- 35:11with direct mutations.
- 35:13We actually did find that there's you
- 35:14know one with a key reputation among
- 35:16these and some did not have the reputation,
- 35:18so it's sort of an interesting
- 35:20question still.
- 35:22And so all of this together,
- 35:26you know we can put together a
- 35:28basic molecular classification
- 35:29of colorectal cancer.
- 35:33OK, so now kind of going to shift
- 35:35gears and start talking a little
- 35:37bit more about mutation testing.
- 35:39So here's another patient.
- 35:41Newly diagnosed metastatic
- 35:43colorectal cancer to the liver.
- 35:46Prior testing showed microsatellite stable
- 35:50tumor and what should you order next?
- 35:58And so in order to, you know.
- 36:00So this is where we come back to the
- 36:03NCCN guidelines and sort of start
- 36:05to understand how is information
- 36:06used and what sort of information
- 36:08is needed for continued treatment,
- 36:11and so patients who have metastatic
- 36:13colorectal cancer should have
- 36:15genotyping forreston draft mutations.
- 36:18And the reason for that is
- 36:21is because there is a.
- 36:23Antibody that's frequently used as part
- 36:26of chemotherapy for colorectal cancer.
- 36:29The targets. The rest raft pathway,
- 36:31and so in order for this antibody to work,
- 36:35rest, and draft have to be wild type.
- 36:40And so this is where this is
- 36:42where this pathway comes in.
- 36:44So here we have EGFR, which then
- 36:49signals downstream into grass and RAF.
- 36:52RAF happens to be the most mutated
- 36:55gene in colorectal cancers.
- 36:57Approximately, you know,
- 36:58up to even 50% of colorectal
- 37:01cancers will have RASK mutations,
- 37:03and they're in order to use setx map as
- 37:07a component of the chemotherapeutic.
- 37:10Regimen.
- 37:12We have to rule out mutations in the
- 37:15tumor because this this antibody will
- 37:18have no efficacy of downstream of that
- 37:22of of of EGFR is an activating mutation.
- 37:27But you can see that we also have,
- 37:29you know there's mutations in
- 37:31various other genes as well,
- 37:32some of which may be targetable
- 37:34and others are not.
- 37:35So how do we test for driver
- 37:39driver for forreston ref?
- 37:41Mutations in colorectal cancer.
- 37:43This has evolved overtime.
- 37:45You know,
- 37:46ten years ago would have
- 37:48been PCR of some sort.
- 37:50And you know,
- 37:52but that has evolved quickly through.
- 37:56Into real time PCR and now primarily
- 37:59next generation sequencing being the
- 38:01standard for doing this type of testing.
- 38:04And so I so after coming to Yale,
- 38:06I got interested in colorectal
- 38:09molecular testing at Yale,
- 38:10and I, you know,
- 38:13sort of.
- 38:14Intersected with with our molecular
- 38:16labs and try to find out like what
- 38:18is going on and so we have two main
- 38:21labs that do CRC molecular testing
- 38:23and they don't overlap too much
- 38:26with each other in terms of the
- 38:28the specific test that they do.
- 38:30So the molecular diagnostics
- 38:31lab does a lot of PCR.
- 38:34For MSI and also single gene
- 38:36testing like graph 4K Ras,
- 38:39they also performed the MLH fund
- 38:41methylation and I'm here just focusing
- 38:43on the role of this lab and CRC testing.
- 38:45I'm not at all going to talk about,
- 38:47you know all the other wonderful
- 38:49things that that lab does and has
- 38:52developed in recent years and
- 38:53then we have the tumor profiling
- 38:56laboratory and the tumor profiling
- 38:58laboratory primarily uses next
- 39:00generation sequencing as a method for
- 39:02detecting mutations and tumor cells.
- 39:04And I'll talk in a lot more
- 39:06detail about that lab, so.
- 39:08You know when I first arrived
- 39:10at Yale in 2011,
- 39:12this was our GI Group back then and
- 39:14I was primarily doing GI pathology,
- 39:17but I I really wanted to expand my
- 39:21clinical practice and I started
- 39:23thinking about maybe I I could join the,
- 39:26you know,
- 39:27one of the molecular labs and
- 39:29after discussing
- 39:30with various people I got support from.
- 39:39There we go. I got support from Doctor
- 39:43Walter and the tumor profiling lab
- 39:45and with doctor Marrows and Doctor so
- 39:48Nards and Doctor James support as well.
- 39:51I was able to join the tumor profiling
- 39:54laboratory as a faculty member.
- 39:56And you know, how did I do this?
- 39:59I mean, this was not something
- 40:01that happened overnight.
- 40:02I joined the laboratories
- 40:04Case Review conference.
- 40:05Just sort of a consensus
- 40:08conference type review of cases.
- 40:11I went to the precision Medicine
- 40:14tumor board for, you know,
- 40:16a while before then joining the roster of
- 40:18people who present at that tumor board,
- 40:20I shadowed the faculty at that time in the
- 40:23German profiling lab and then finally.
- 40:26I was able to get a block of six
- 40:29weeks to be able to do a rotation
- 40:31sort of identical to what a fellow
- 40:34would do and learned all the different
- 40:37aspects of the tumor profiling lab.
- 40:40And so primarily next generation
- 40:44sequencing is the platform that is
- 40:45used by the tumor profiling lab and
- 40:47this is an ultra high throughput,
- 40:49scalable, fast method of sequencing DNA,
- 40:52and it's, you know.
- 40:54I I fit the whole sequence of events
- 40:57of how next generation sequencing
- 40:59works on one slide,
- 41:00but it's it's it's a very busy slide
- 41:03and so there's there's different
- 41:04steps that have to be done.
- 41:06First sample has to be prepared,
- 41:08DNA has to be extracted.
- 41:10Library preparation and templating
- 41:12has to occur.
- 41:14Sequencing has to occur in the
- 41:16sequencing is sort of a bit of a
- 41:18magical step where it's actually, you know.
- 41:22It's a.
- 41:25Electric, you know it's a.
- 41:26It's a electronic signaling
- 41:28or electronic sequencing.
- 41:30Basically that that occurs and
- 41:32it generates a ton of information
- 41:35by informatics is a big big
- 41:37step and we have several people
- 41:39working on that who actually.
- 41:42Go through all of these steps and
- 41:44give us the annotated mutations that
- 41:46are found in a particular tumor,
- 41:48and then we have to interpret
- 41:50those those variants and we use
- 41:53different types of databases to to
- 41:55do that and just to sort of make
- 41:57sure that everyone sort of knows
- 41:59most of the stuff happens in the
- 42:01Department of Laboratory Medicine.
- 42:03The variant interpretation
- 42:04is what the faculty do,
- 42:06and we do that and and it's the
- 42:10pathology faculty who do that.
- 42:11And so.
- 42:12How is NGS actually used,
- 42:15and what are the advantages
- 42:17of it so you know,
- 42:18with NGS you can sequence
- 42:21really any area that you know.
- 42:24Almost any area that is of interest
- 42:27and the advantages that multiple
- 42:29areas can be sequenced all at once,
- 42:32like massively,
- 42:32and so you know when you look at crass.
- 42:36Yes,
- 42:36there are some common hotspots
- 42:38that are really interesting
- 42:40and recur quite frequently,
- 42:41like a code on 12 or 13,
- 42:43but there's a lot of other smaller
- 42:45hotspots at 146 at 1:17 at 61,
- 42:48and so with NGS we're able to sequence
- 42:51all of the hot spots at once,
- 42:53and so we have one panel.
- 42:55For.
- 42:58That looks at 50 different hotspots
- 43:00or I should say looks at 50 genes
- 43:03at various hotspots and this is the
- 43:07panel that's used for diagnosing.
- 43:10Metastatic colorectal cancer and how
- 43:14does the entry of data come back to us?
- 43:17It's actually.
- 43:19Comes back in an Excel style
- 43:22spreadsheet which can be somewhere
- 43:24you know this is a simple.
- 43:26Summary of that result.
- 43:27So here we have, you know, for example,
- 43:31TP 53 has a C DNA mutation that
- 43:35replaces G2AG to an A at nucleotide 818,
- 43:40which then leads to a change in the
- 43:44protein of arginine to 73 to a histidine.
- 43:47And what's also important is that
- 43:50this particular position was.
- 43:54Stop.
- 43:54It was read almost 2000 times,
- 43:58so this position was was found in 2000.
- 44:03Let's look was seen at least 2000 times,
- 44:05and 20% of those reads showed this variant,
- 44:10and so here you can see what that
- 44:13looks like in in the I GB program.
- 44:17So this is the genomics viewer that we
- 44:19used to look at the actual mutation.
- 44:21So here we have the K rest gene.
- 44:23With this particular mutation,
- 44:25and there's each of these bars
- 44:28represents one of these reads
- 44:31that forms the coverage and.
- 44:33That she represents the change at
- 44:36that particular meeting, and we have.
- 44:38And they're color coded for
- 44:40reverse sent forward reads.
- 44:44And so this is what a cancer mutation
- 44:48hotspot panel result looks like.
- 44:50There's an add no carcinoma
- 44:52estimated 30% malignant cells and
- 44:56we have a BRAF V600E mutation.
- 45:01And our other pathology records
- 45:03show that this was an MSS cancer,
- 45:07and so this brings up an interesting
- 45:10subject of the reputation in MSS.
- 45:13Colorectal cancers.
- 45:13And this is an interesting subtype of
- 45:16cancer that does not neatly fit into
- 45:18our current models of personal genesis.
- 45:21These tumor types are.
- 45:25Relatively rare on the order of,
- 45:27you know, maybe 5-4 to 7% depending
- 45:30on what study you read, and you know.
- 45:34Unlike other tumor types,
- 45:36that kind of neatly fit into our
- 45:39knowledge of of precursor lesions, etc.
- 45:41We don't really know how these tumors
- 45:44arise and what is the what is the primary
- 45:46sort of starting point for those.
- 45:49But the most interesting thing is that
- 45:51they do now have a therapeutic option,
- 45:54and so recognizing these tumors.
- 45:56Is important and I'm working
- 45:59with our current fellow Dr each,
- 46:02as well as some others and looking at.
- 46:08MSS CRC's. Looking at some of those
- 46:10molecular features to add to this knowledge,
- 46:12and this is this is the most recent.
- 46:19This is that this is a study that
- 46:22described that tablet therapy,
- 46:23the doublet therapy includes
- 46:26this EGFR targeted treatment,
- 46:28such as a tax map,
- 46:30combined with a BYREF inhibitor.
- 46:32Initially, this was also had a
- 46:34component of a MEK inhibitor,
- 46:36but within a few months of
- 46:39this paper being published,
- 46:41they've they've decided that
- 46:43the doublet has just as much
- 46:45efficacy as the triplet therapy.
- 46:47And so this is now becoming a
- 46:50standard of of care for BRAF.
- 46:55Mutated by MSS tumors.
- 46:59Alright, so moving on to a different patient.
- 47:01This was a patient #4 who had a combined
- 47:04hepatocellular cholangiocarcinoma.
- 47:06It was MSS and now his
- 47:09progressive disease and.
- 47:10As a pathologist, do you order anything?
- 47:13The answer is no, you don't.
- 47:16It's kind of a trick question.
- 47:18It's the oncologist who may order
- 47:20a comprehensive NGS panel and
- 47:22that panel at Yale is on combine.
- 47:25And so the anchor mine is
- 47:27a much bigger panel.
- 47:29It sequences 87 jeans at various hotspots.
- 47:34There's also 48 genes
- 47:36that are fully sequenced.
- 47:38These are mostly the tumor supressors.
- 47:41We were also able to look at
- 47:43amplification of a number of genes
- 47:45as well as a number of gene fusions
- 47:47and so the anchor mine panel is
- 47:49used primarily in patients who
- 47:52have stage four disease and have.
- 47:54Failed conventional chemotherapy and
- 47:56it's really to identify mutations that
- 47:59may be therapeutic therapeutically.
- 48:02Targetable in a specific manner,
- 48:04or may may have implications
- 48:07for clinical trials as well,
- 48:10and we what what's unique about the
- 48:12Yale practices that we use a germ
- 48:15line control to determine the somatic
- 48:17status versus hereditary status
- 48:18of any variance that we identify.
- 48:21And so,
- 48:22so this was actually two patients
- 48:24with in this example, and.
- 48:26And we ended up publishing
- 48:28this short case series.
- 48:31With a former fellow at Yale,
- 48:34so one of the patients was at 59 year
- 48:36old woman and she had a combined
- 48:40cholangio carcinoma carcinoma.
- 48:41You can see that HTC component here.
- 48:44The collector component there.
- 48:46She had a personal history of
- 48:48breast cancer in the past and
- 48:50the thyroid cancer as well,
- 48:52and then she had a fairly extensive
- 48:54family history of cancer of various
- 48:56cancers and then patient #2,
- 48:58excuse me is a 62 year old man
- 49:00and he didn't have prior cancers.
- 49:03But he did have a sister who had
- 49:05both breast and uterine cancers,
- 49:06who had died of those cancers.
- 49:10And these are the alkaline results
- 49:12for those two patients.
- 49:14Both patients ended up having
- 49:16a bracket 2 mutation.
- 49:20And.
- 49:22Patient one has this
- 49:25pathogenic nonsense mutation,
- 49:26so it's premature leads to premature
- 49:28termination of the protein,
- 49:30and this was found to be both in the
- 49:33germline and in the tumor and patient.
- 49:35Two had two Broadcom mutations.
- 49:38One of these mutations is a
- 49:40pathogenic splice site mutation and
- 49:42this was found to be again in the
- 49:44patients germline sample as well
- 49:46as the tumor sample and then there
- 49:47was a second somatic mutation in
- 49:49bracket two as well and so based
- 49:51on these results a diagnosis of
- 49:53heritage Terry breast cancer.
- 49:55In a variant,
- 49:56syndrome can be made in both
- 49:59patients and you know it's it's one
- 50:01of these situations where I'm like,
- 50:03well, you know people,
- 50:04could you know maybe the patient
- 50:05with breast cancer should have been,
- 50:06you know, found to have this previously.
- 50:08I don't know. Not really sure.
- 50:11You know what, you know.
- 50:13When patients get screened for
- 50:15breast cancer exactly.
- 50:17For the syndrome, but looking at you
- 50:20know malignancy risks and patients
- 50:22with this particular syndrome
- 50:25combined cholangiocarcinoma HCC or
- 50:27is not really anywhere on that list.
- 50:30So you know, maybe they're related,
- 50:31you know, pancreatic.
- 50:32You know it's a biliary type cancer.
- 50:35Maybe that that that might be a
- 50:37hint that that could be part of it.
- 50:39So here's an example where we can
- 50:43really impact patient results,
- 50:46patient families by detecting mutations.
- 50:52And you know what?
- 50:53The risks that are associated
- 50:55with them in tumors that are not
- 50:58necessarily expected for that syndrome.
- 51:00And in addition to that,
- 51:03this also leads to the possibility
- 51:05of a specific type of therapy,
- 51:08and so in brocco mutated tumors,
- 51:10the use of carp inhibitors is.
- 51:14Is a possibility where you know.
- 51:19Where you know if you Park is an
- 51:22enzyme that is involved in DNA repair
- 51:26and if you include if you add up our
- 51:29PIN hitter and hit this enzyme in
- 51:32tumors that have a mutated BRACA.
- 51:342 homologous recombination cannot
- 51:36be done and these patients undergo.
- 51:40You know these tumors undergo cell death
- 51:43and something called synthetic lethality.
- 51:45And there are now a lot of
- 51:47carpet hitters that are.
- 51:48Clinical use primarily for
- 51:50ovarian and breast cancers,
- 51:52but they definitely would be an
- 51:54option for both of these patients
- 51:56if if they should recur.
- 51:58For their tumor, and this is another example.
- 52:01That was a different publication
- 52:03that was also interesting,
- 52:04and this was a 63 year old man who
- 52:07had a gallbladder respected and
- 52:08this was initially seen else not at
- 52:11not centrally Yale and the initial
- 52:13diagnosis that was made was Edna carcinoma.
- 52:15Several, you know months later.
- 52:18The page you know,
- 52:21the clinician oncologist ordered,
- 52:23and she S testing and MSI testing,
- 52:26and it came to us.
- 52:28For assessment and between the morphology
- 52:32and the results from the oncoming testing,
- 52:37the diagnosis was revised to Miso,
- 52:39thi Lio Ma,
- 52:40and that's because this particular tumor,
- 52:43one of the reasons was that this
- 52:45particular tumor showed about 1 mutation,
- 52:47and again there's two of them.
- 52:49There's one mutation that was seen both
- 52:50in the tumor and in the patient's blood,
- 52:53and a second back,
- 52:54one mutation that was found
- 52:55in just the tumor.
- 52:56So here's an example of somebody again.
- 52:59Has a germline first hit and that one
- 53:01and the tumor there's a second hit in
- 53:05in the in the second allele of BAP one.
- 53:12Doctor Shelper I see your question.
- 53:14I can come back to it a little bit later
- 53:16and so for this particular patient we
- 53:18can make a diagnosis of Bab 1 trimmer
- 53:21for Disposition syndrome and you know,
- 53:23looking at this patient pedigree,
- 53:24there was actually quite a lot of
- 53:26cancer in this patient syndrome.
- 53:28And you know, again,
- 53:29you know we can sort of allow this
- 53:31family to be able to be tested for it
- 53:34and and now they can start potentially
- 53:36screening for some of these cancers, etc.
- 53:41And and so.
- 53:43You know the concept of being able
- 53:45to do genetic findings that are
- 53:48discovered through online testing.
- 53:50Is is something that we are working
- 53:53on in collaboration again with our
- 53:55genetics clinic and we looked at 123
- 53:59patients who had a known pathogenic
- 54:02variant and you know 2/3 of them.
- 54:08We're not known prior to the testing
- 54:10with alkaline that that that they
- 54:12had in pathogenic mutation in their
- 54:14germ line that will impact either
- 54:18their family members or options for
- 54:20therapy and then doctor Shelper.
- 54:22You mentioned that in this case the
- 54:25germ line was it is a little bit low.
- 54:28It would be expected to be at.
- 54:3040% or 50% if it was a heterozygous
- 54:33germline variant,
- 54:34it's within range of what we see with.
- 54:39With.
- 54:40With MGS testing,
- 54:42so sometimes there can be a little
- 54:45bit of skewing that happens with NGS
- 54:47and you may not get a perfect number,
- 54:50but we we typically accept these results.
- 54:57And Doctor Robert asked another question.
- 54:59The diagnosis of change from the
- 55:01adenocarcinoma to miso, thi Lio Ma?
- 55:03It was based by both.
- 55:05Really it was based on both.
- 55:07So when they add note when this
- 55:10gallbladder came over we were able to.
- 55:13So I'll say this was all Doctor Ilkay who
- 55:16initially raised alarm about the diagnosis.
- 55:19She she thought it was an odd looking add,
- 55:21no carcinoma, quote, UN quote,
- 55:23and so she ordered additional
- 55:25immunostains to check.
- 55:26And and at the same time NGS was
- 55:29being done with anchor mine.
- 55:31So basically,
- 55:32when all of those results came out,
- 55:35you know it was coordinated
- 55:38and the change was made.
- 55:40So sort of a combination.
- 55:41It was not one or the other.
- 55:46OK, so in the last three minutes last
- 55:49patient, so this was a patient who
- 55:51had a new diagnosis of metastatic
- 55:54non different carcinoma and the
- 55:56question is what do you order?
- 55:57And really again it's a tricky question
- 56:00because NGS does not really have a
- 56:03huge role in the diagnosis of any
- 56:06neuroendocrine tumors or neoplasms.
- 56:08Neurocrine tumors tend to be
- 56:10diagnosed by morphology as either well
- 56:12differentiated or poorly differentiated.
- 56:14And you know, poorly differentiated
- 56:17ones tend to have a lot of P53RB
- 56:21mutations or CDKN 2A mutations,
- 56:23whereas the mtor pathway tends to
- 56:26be altered in the wild if tumors,
- 56:28and so NGS that targeted therapy does
- 56:31not really have a huge role in this.
- 56:33Nevertheless,
- 56:34on combine was ordered for this patient.
- 56:37And so this is from the hepatitis
- 56:40specimen and we estimated 90% malignant
- 56:42cells within this tumor sample and over
- 56:46150 mutations right outside in this tumor.
- 56:49And you know, this is something that,
- 56:51like when we get one of these results
- 56:54on the tumor profiling lab service.
- 56:56We just like want to start crying because how
- 56:59do you assess 150 importations in one tumor?
- 57:03And you know you've got like 20 other
- 57:06tumors to look at, so you kind of.
- 57:08You know you sort of gain experience
- 57:10and you figure things out anyway,
- 57:13so we had 15 mutations there.
- 57:16That were, you know,
- 57:17sort of significant.
- 57:18There's 140 others that were maybe
- 57:21like a little bit more vus types,
- 57:24and so basically this is a tumor that's
- 57:27consistent with hypermutation and.
- 57:30How does hyper mutation occur in cancer?
- 57:33There's multiple causes of it.
- 57:35MSI is one of those we've already spoken
- 57:38about MSI quite a bit and others could
- 57:41be mutations and pull or pull D and
- 57:44Neurocrine tumors are not commonly.
- 57:49Do not commonly show MSI high status.
- 57:52Maybe only a handful of those cases.
- 57:55And maturity of.
- 57:58You know MSI high tumors are
- 58:00sporadic in nature,
- 58:01so you know we want to execute lynchings.
- 58:03M in this patient and
- 58:05thankfully none of these.
- 58:06None of these mutations were germ
- 58:08line in this particular patient and
- 58:10just looking deeper into literature
- 58:14you know what do we know about
- 58:16hypermutation and nerve tumors you
- 58:18know and does MSI contribute to that?
- 58:20And at least then one study there seems
- 58:22to be a contribution of them aside,
- 58:24hypermutation in our consumers and
- 58:26another study also found a fairly
- 58:29high number. Tumors that had.
- 58:33Mr.
- 58:33That was unstable but not a
- 58:36lot of detail about it,
- 58:38and the point is that maybe it doesn't
- 58:41really matter what the cause of the MSI
- 58:43in this patient is, but now we know that.
- 58:46Or the hypermutation.
- 58:47But now we know that there's a
- 58:49response to PD one inhibition.
- 58:50That's an option for him,
- 58:52and this is an example of a
- 58:55patient who responded to Pembroke.
- 58:59You know who had a MSI High Nordic rent
- 59:03tumor and this is something that's,
- 59:06you know this.
- 59:07This expanding utility for using MSI to
- 59:10predict response to PD one is
- 59:14a relatively recent finding.
- 59:16And we can also think about MSI.
- 59:21As measured by NGS,
- 59:22this is an emerging by informatics tools.
- 59:24There are numerous computational methods
- 59:26that can be used for NGS detection
- 59:28and just in the interest of time I'm
- 59:30going to skip through some of these.
- 59:32We did look at.
- 59:33We did look at one of these methods to be
- 59:36able to tell NGS with our former fellow,
- 59:40and we did find that this is a
- 59:42specific but non sensitive method,
- 59:44at least using the oncoming NGS data and so.
- 59:48In this particular patient,
- 59:50although the mantis was negative for MSI,
- 59:52you know we still have questions
- 59:55about you know what might have
- 59:57been the cause of this patience.
- 59:59Anyway, I'm going to skip the next couple
- 01:00:01of slides here and just get to the end.
- 01:00:03If any of you are interested in
- 01:00:04in more of these types of cases,
- 01:00:06please come to the precision Medicine
- 01:00:08tumor board where we review all kinds
- 01:00:10of tumors with all sorts of findings,
- 01:00:13both germline and somatic,
- 01:00:14and determine what best causes are.
- 01:00:17So, in summary,
- 01:00:18I hope you guys have seen how I've
- 01:00:20gone through this mandering path
- 01:00:22of being a GI and liver surgical
- 01:00:25pathologist into incorporating molecular
- 01:00:27pathology into my practice and into my.
- 01:00:31Research and focusing on
- 01:00:33patients results and.
- 01:00:36And outcomes,
- 01:00:37and hopefully in the future
- 01:00:40we can coordinate some of this
- 01:00:42information more seamlessly and
- 01:00:44have an integrated practice where.
- 01:00:47This information flow happens easily
- 01:00:50and accessibly to everyone and so.
- 01:00:54I'd like to thank everyone I you know, AM.
- 01:00:58Moving on to some new new things
- 01:01:01in the department as the Director
- 01:01:03of Quality and Patient Safety cell
- 01:01:05be leaving behind some of this,
- 01:01:07some of this research that I'm doing here,
- 01:01:09but I'm sticking around and I'm looking for.
- 01:01:15You know collaboration with everybody,
- 01:01:18and in this new endeavor.
- 01:01:21And that's it.
- 01:01:22That's yeah,
- 01:01:22I'm sorry for going over a little bit,
- 01:01:25but I'm happy to take some
- 01:01:27additional questions at this time.
- 01:01:30So we have about 84 people logged in
- 01:01:33and we are well over the time limit,
- 01:01:38but maybe a quick one or two questions.
- 01:01:42Please unmute yourself and ask.
- 01:01:47So I can start with Joanne, you know?
- 01:01:50Joanne, thank you for this.
- 01:01:52Very interesting you know seminar.
- 01:01:55I think this is you as your last set.
- 01:01:57So I point out this is exactly
- 01:01:59probably the future direction of
- 01:02:01future practice of our pathologies.
- 01:02:04So my question to you is if we are from from
- 01:02:06your personal experience and do you feel?
- 01:02:09I mean if whatever you can share with us,
- 01:02:13some of your personal experience,
- 01:02:14you know when you are not about
- 01:02:16certain that you did not.
- 01:02:17Through the Molecular Pathology
- 01:02:19fellowship you are just, you know,
- 01:02:21surgical pathologists and then decided to.
- 01:02:24You know to practice molecular
- 01:02:25pathology what you know.
- 01:02:27What's your experience you think is doable?
- 01:02:29I mean certainly it's doable.
- 01:02:30You prove it.
- 01:02:31But what I'm saying and it obviously
- 01:02:32you know and it hurdles any sort of
- 01:02:35insights you may have for other sort
- 01:02:37of aspiring surgical pathologies that
- 01:02:40may thinking that goes through the,
- 01:02:42you know, the way you have guns.
- 01:02:44Yeah, yeah, absolutely.
- 01:02:45I mean, I hope other pathologists
- 01:02:47can join me in in this way as well.
- 01:02:50I I think challenge is that
- 01:02:52there is more molecular work.
- 01:02:54Then there are molecular
- 01:02:56trained molecular pathologists,
- 01:02:58so there is need for you know additional
- 01:03:01expertise in this area and I think
- 01:03:04in addition the world of molecular
- 01:03:07pathology I think is changing rapidly
- 01:03:10more rapidly than the fellowship
- 01:03:12training can sort of keep up with
- 01:03:16and you know a lot of these end results.
- 01:03:19You know this is all in the last five years.
- 01:03:22Fellowships can change fast
- 01:03:23enough to sort of incorporate.
- 01:03:25That aspect, and.
- 01:03:29And you know, I you know,
- 01:03:31I personally had a strong interest in cancer.
- 01:03:33That I, you know, goes back to you,
- 01:03:35know my PhD days.
- 01:03:37So I was sort of primed to
- 01:03:40learn this material quickly.
- 01:03:42But it can be done, I think with.
- 01:03:46You know what?
- 01:03:47So one thing that I did I I always like
- 01:03:49to think I always like to say that I
- 01:03:51actually did exactly what a fellow does.
- 01:03:53I did a six week rotation at TPL at that's
- 01:03:56what a fellow in molecular pathology does.
- 01:03:58They do a six week rotation in
- 01:04:00TPL and I'm focusing on just that
- 01:04:03aspect of molecular pathology.
- 01:04:04I'm not, you know,
- 01:04:06I I let others worry about you,
- 01:04:08know the fish.
- 01:04:09The MLH 1 methylation the PCR,
- 01:04:12you know, I, I trust the you know
- 01:04:15other labs to do their part so I'm.
- 01:04:17You know,
- 01:04:18with a narrow focus like that,
- 01:04:20I think it's quite possible for many
- 01:04:22pathologists sort of interact with this,
- 01:04:24and I think in addition,
- 01:04:26we really need to expand our teaching
- 01:04:28so that everybody can sort of chip in
- 01:04:32small things in in this in this endeavor.
- 01:04:36So just by increasing our,
- 01:04:38you know our ability to teach the future
- 01:04:41generations some of this material.
- 01:04:43I think it's just it's a.
- 01:04:44It's a rapidly evolving field.
- 01:04:47And and I think we need to be.
- 01:04:51Creative and how we approach all the
- 01:04:54work that this field is generating.
- 01:04:58Thank you.
- 01:05:08Well, if there are no questions. I'll let.
- 01:05:14It was a great shock Joanna I I think
- 01:05:17as a surgical pathologist,
- 01:05:19I really appreciate the bringing in
- 01:05:21of integration with molecular and I.
- 01:05:24I think we would all welcome
- 01:05:26that integrated report and
- 01:05:28the learning that we can gain
- 01:05:30from you and your colleagues.
- 01:05:32So I I think that we will be
- 01:05:35very supportive of this and
- 01:05:36I want to thank you for giving
- 01:05:38such an interesting talk.
- 01:05:39So patient focused. That I think,
- 01:05:43makes it quite clear that the time is now
- 01:05:46to do this, yes, so you and I will
- 01:05:48have to talk about the colon cancer,
- 01:05:51integrated reports and how we can
- 01:05:52bring that to our service for sure.
- 01:05:57And we also want to talk
- 01:06:00about integrated report.
- 01:06:01In reports in head and neck cancers,
- 01:06:04absolutely all of them.
- 01:06:06Thank you so much.
- 01:06:10Alright, thank you everybody,
- 01:06:13thank you. Thank you.