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Genetics of Renal Cell Carcinoma: Paving the Way for the Next Generation of Therapies

Why don’t the various medications work better for RCC?  Why do some patients do well, and others so poorly?  Why is it so hard to choose the right medicine?

This lecture explains why patients  and doctors must play the guessing game in treatment. It may be the most important lecture in this blog, and provides an explanation as to why RCC cancers behave so differently, even those variants  with similar pathologies. (My notes are in italics, like this, added to help with this complex discussion…I hope.)

Presented by Dr. James Brugolas, MD, PhD.: Kidney Cancer Program Leader Associate Professor of Internal Medicine & Developmental Biology; University of Texas Southwestern Medical Center

http://www.chemotherapyfoundationsymposium.org/mobile/player.php?id=476

“I am going to talk to you today about the genetics of kidney cancer and how I believe it is paving the way for the next generation therapies. There are no significant disclosures.Brug 1 What is the ProblemWhat is the problem? This is a problem that we are well aware of some nowadays. We’re using one drug for all patients with kidney cancer.   You may imagine that these are all patients with metastatic renal cell carcinoma. But it is a heterogeneous population. Some have the red tumor, some of them the green tumor, and the drug may work with a subset of patients, but it may not work for another subset of patients.(Left half of the slide with the meds not reaching the patients with GREEN tumors.)

We should be evolving to a paradigm where patients with different tumors are treated with different drugs. (Right half of slide shows Drugs A and B going to different subsets of patients.)BRUG 2 Kidney Cancer subtypesIn the context of renal neoplasms , as you are well aware, we have kidney cancer with clear-cell carcinoma which accounts for the vast majority (75%) of that, and that’s going to be the focus of the first part of the talk.

BRUG 2 EDITSCaptureThe work from the Sanger Institute by Andy Futeral and Michael Stratton led to the identification of mutations in the PolyBromo1 gene. Polybromo1, like VHL, the most commonly mutated gene in clear cell renal cell carcinoma, is a two-hit tumor suppressor gene. That means both copies are mutated in tumors. They identified through truncating mutations in approximately 41% of clear-cell RCC. PolyBromo1 encodes BAF 180, which is a component of a nucleosome modeling complex which may regulate, among other processes, transcription.” (Peg & Wikipedia say that transcription is the first step of gene expression, where DNA is copied into RNA, giving instructions. Pretty basic cell info.)

BRUG 3BAP1 loss defiens new class of RCCCapture

“Work from my laboratory led to the discovery of another gene mutated in RCC, the BAP1 (BRACA1 associated protein-1) gene. Like the BPRM1 and VHL, BAP1 is a two-hit tumor suppressor gene, but it is mutated in only about 15% of sporadic clear-cell RCCs.

This work was done focusing on tumors that were of high grade. Indeed, we found there was a correlation between BAP1 loss and high grade, and also activation of the mTOR1 pathway. BAP1 encodes a nuclear deubiquitinase. Of greatest interest, mutations in BAP1 and BPMR1, we found, are largely mutually exclusive. This is shown this more detailed the next slide.

BRUG 4Mutation in BAP1 ^ PBMR1 mut excluWhat you are seeing here are 176 tumors, each in a row. These are tumors that have a deletion in PBMR1, these are tumors with the insertion, this with a point mutation (referencing the various symbols P). All the tumors in blue are tumors that have a mutation. As you can see most of the tumors, we see with PBRM1 mutations do not have mutations in BAP1. (Column 4 has many BAP1 mutations.)

(in last column) Here you have some tumors with mutations in BAP1, and we only identified three tumors that had mutations in both genes. (Very end of column 4) The probability of having mutations in both genes was statistically significant. Based on the individual mutation probability, we would have expected 13 tumors to have both genes. Only three were found, suggesting that BAP1 and BPRM1 mutations are largely mutually exclusive.

BRUG 5BAP1 & PBRM1 meta analWe went on to performing a meta-analysis. This is looking at data from that Beijing Genome Institute, at Memorial Sloan-Kettering and this from the TCGA (The Cancer Genome Atlas). As you can see, even though the numbers are small, the numbers of tumors with mutations in both BAP1 and PBRM1 was reduced, compared to the expected number of tumors based on the individual mutation frequency, and the p value was statistically significant.BRUG 6BAP1 & PBRM1 gene signatureI’m going to go through these and not spend much time, but suffice it to say that that we found that these tumors that have had mutations in BAP1 have a characteristic gene expression signature, and the tumors that have mutations in PBRM1 also have a characteristic gene expression signature. These gene expression signatures do not overlap. These are tumors that have different gene expression patterns and different biology.  (Per Peg: this shows that these are biologically different tumors. Notice the different patterns of red and blue below.)

BRUG 7 BAP1 & PBRM1 ex  diff SMALL

We think this establishes a foundation for the first molecular genetic classification clear-cell RCC. In our series, 55% have mutations in PBRM1, and 15% of the tumors have BAP1, and including 3% have mutations in both.  (The balance are wt, wild-type, meaning as it occurred in nature, not mutated.) BRUG 8Fdn Mole Gene sign ccRCC We also observed that there is a statistically significant correlation between mutations in BAP1 and high grade (tumors), and mutations in PBRM1 in low-grade (tumors).

So that let us to propose the following model. This is a model based on the fact that, very interestingly, VHL, BAP1, and PBRM1 are all located on chromosome 3. In fact, the short-arm of chromosome 3, and this is an area that is deleted in the majority of patients with von Hippel-Lindau-associated renal cell carcinoma, as well as in the majority of sporadic renal cell carcinoma, depicted here in blue.  (VHL associated RCC is an inherited type of RCC, not arising from a mutation…but along the same chromosome.)

BRUG 9  BAP1 & PBRM1 on chromo 3p VHLYou can imagine that with a single deletion, the kidney cell is losing, in fact, four copies or one copy of these four different tumor suppressor genes, the BAP1, PBRM1 and VHL.BRUG 10 VHL mutat high low grade diff

We have proposed the following model. We believe that renal cell carcinoma, and this is consistent with data from Gerlinger and colleagues, that it begins with an intergenic mutation in the VHL gene. And this is followed by loss of 3p, with a concomitant loss of one copy of all of these tumor suppressor genes. We then think that a mutation in PBRM1 leads to the loss of PBRM1 function, which is a two-hit tumor suppressor gene and low-grade tumors, whereas the mutation in BAP1 is associated with the development of high grade tumors.

REFER to ABOVE PIE CHART re High and Low Grades

This model also predicts that patients with BAP1 and PBRM1 deficient tumors may have different outcomes. So we simply took those patients whose tumors we had analyzed and asked what happens to their outcomes. (The UTSW and TCGA cohorts reference tumors from different institutions. Blue lines are the PBRM1 deficient tumors, and red lines the BAP1 tumors. The lines which fall the quickest show poorer overall survival.)BRUG 12 BAP1 & PBRM1 diff outcomesAs you can see here (LEFT), we found that patients with PBRM1 deficient tumors had a significant better Overall Survival than those who had BAP1 in their tumors, which had a Hazard Ratio for that of 2.7.

We did a similar analysis with the TCGA cohort, and we found (RIGHT) essentially the same result in the same hazard ratio of 2.8, indicating that BAP1 mutant tumors are associated with worse outcomes in patients. This data has now been reproduced by Hakimi and James Ying at Memorial Sloan Kettering, as well as the TCGA with their own analysis and our colleagues in Japan and Tim Eisen.

BRUG 12 Limit of SequencingThere are some limitations of sequencing. We all like next generation sequencing, but it has some limitations. First, it focuses on DNA. Secondly, it uses pooled material. Thirdly, it has reduced sensitivity which is a consequence of contamination by normal cells. In addition, a negative result does not guarantee that there is normal function. There is poor discrimination of subclonal mutations in different cell populations. So as a consequence of using poor material, we cannot tell whether these mutations are found in the same cells or different cells. Typically, it involves fresh frozen samples which are reduced in numbers, and consequently has limited power for doing some analysis.

Interestingly enough, immunohistochemistry (IHC), which we’ve use for a long time is a lot more precise. This is because actually you get information at the cellular level, and you get information about the protein. I mentioned to you that BAP1 is a two-hit tumor suppressor gene, which basically means when it gets mutated, you lose both copies.BRUG 14 dev of BAP1 IHC testAs you can see here–this is the same series showed before. These are here in blue the tumors that had mutations, in the second column, you can see blue and brown, the results by immunohistochemistry. That is done by IHC. And BAP1 is a nuclear protein, as you can see in these beautiful nuclear staining.

The bottom line is the majority of tumors that had mutations (referencing blue column data points) had lost BAP1. There were two tumors with point mutations where we were able to detect the protein. But there were three additional tumors we could not detect protein, but where there was no protein. If there is no protein, there cannot be functioning.

The rest of the tumors, with one exception, were all positive. So compared to mutation analysis, in fact, there is positive predictive value is better and the negative predictive value is pretty similar.

BRUG 15BAP1 loss assc w red CSS ccRCC

We have used this immunohistochemisty test in conjunction with the Mayo Clinic, looking at their registry with over 1300 with localized ccRCC. As you can see, looking here with people with specific RCC survival, patients with RCC tumors that have BAP1 positive tumors have significantly better survival outcomes than those who have BAP1 negative tumors, again with a Hazard Ratio of approximately 3.

BRUG 16Evalu of PBRM1 by IHC cohortNow in the same cohort we looked at BPRM1, which like BAP1 in a two-hit tumor suppressor gene, and we find no significant differences.Brug 14Now in the same cohort we looked at BPRM1, which like BAP1 in a two-hit tumor suppressor gene, and we find no significant differences.

Importantly, this test allows us to identify tumors that are simultaneously mutated for BAP1 and PBRM1. This is important.BRUG 17a IHC ids tumors UpperSlide A                                                                                                 Slide B  

(This slide in presented in two parts to help understand lecture.)
Upper half of slide showing stained pathology images.)

I am going to show you look at this tumor over here (upper left path image A) you can see that the tumor cells, there are some that have brown nuclei, but these are the endothelial and the stromal cells (along the edge of the white). The tumor cells are negative for BAP1.

This is the immunohistochemistry (upper right path  image B) for PBRM1, where we find the same thing,where the tumor cells are negative for PBRM1.

BRUG 17b IHC PathSLIDESlide C                                                                                                                  Slide D

Now (left path image C) compare these tumors with these images below. You can see here that the tumor cells positive for BAP1 in this area (the upper right corner of the path image C) and they are negative (in the lower left corner of Slide C), where you can see specific nuclei which look blue over there.

Now if you look at the parallel section (Lower right path slide D) you can see the area that was BAP1 positive (left hand side???D) is actually also PBRM1 negative, and the area which was BAP1 negative is actually PBRM1 positive.

So what you have over here (in the upper slides A & B) is a tumor which has lost BAP1 and PBRM1 in the same tumor region, the same cells. The tumor has lost BAP1 and PBRM1 in independent regions. Obviously these tumors will be acting differently and the tumor we are most interested in is this tumor type (in the upper left image A).

BRUG 18 IHC BAP1 & PBRM1 ids 4 sutypes ccRCCSlide should include quote “BAP1 and PBRM1 do NOT predict outcomes independently of SSIGN”

You have seen in our immunohistochemistry test. We believe we can separate clear cell renal cell carcinoma into four different molecular subtypes. This is looking at Mayo registries, where the patients with best outcomes are those whose tumors are well-typed for PBRM1 and BAP1. Then you have 2) patients that have tumors which are deficient for PBRM1, 3) patients that have tumors that are deficient for BAP1, and 4) patients whose tumors are deficient for both. As you can see the Hazard Ratio is 1.3, 3.2 and 5.2, respectively.

As I mentioned to you at the outset, that these tumors were underrepresented and indeed in this very large cohort, we found a very large significant underrepresentation with 1.8% of the tumors being double mutant, compared to 5.3% (which would been expected) with a very highly significant p value, again indicating there is mutual exclusivity–for reasons we do not yet understand.

Importantly BAP1 and PBMR 1do not predict outcomes independently of SSIGN. SSIGN is the nomogram created by the Mayo Clinic, which is based on Stage, SIze, Grade, and Necrosis. This is the SSIGN nomogram; this is the independent validation. You can see the curves separate beautifully, depending upon the score.

BRUG 19 Nomogr vs BiologyBRUG 20 Nomo vs Bio ANIMACapture

Now another question I submit to you. Should nomograms trump biology? In other words, if they live the same, “What do I care?” That has been the traditionally the thinking in the clinic. But look at these animals. A bullfrog and a grizzly bear also live about 30 years. However, they’re very different. The same is true for cottonmouth, a beaver or hummingbird or a newt. So even though they live the same, they are actually quite different!

We should be probing deeper and in fact, they should be dealt with differently!

BRUG 21ccRCC per genes

I believe that clear-cell renal cell carcinomas are in fact divided for at least four different subtypes. There are tumors that are wild type for both BAP1 and PBRM1, tumors that are PBRM1 deficient, tumors that are BAP1 deficient, and tumors that are deficient for both. In the future we are going to see different treatments for different tumor types.

BRUG 22 Conclusions

In conclusion, the discovery of BAP1 and PBRM1 mutations in clear cell renal cell carcinoma, how they relate to each other, and how they affect outcomes establishes the foundation for the first molecular and functional classification of sporadic ccRCC.

These two genes define for distinct subtypes, which I just went over and you have the Hazard Ratios and p-values written down there. These two tumors are not only associated with different outcomes, but they are also associated with different activations on the mTOR1 pathway and gene expression. Finally we identify mutations in BAP1 which define a novel clear-cell renal cell carcinoma syndrome. I have forty seconds left!BRUG 23 nnRCC graphic

I will go through these very quickly. Suffice it to say, we have also done molecular genetic analysis in non-clear-cell renal cell carcinoma, papillary, chromophobe, oncocytomas, This is now in press in Nature Genetics.

We found that papillary clear-cell carcinoma have more mutations than clear cell carcinoma, whereas chromophobe and oncocytomas have significantly lower mutation burdens, which is depicted there.

BRUG 24 Intr gen analy subtype RCC

These are some genes we found overrepresented– five seconds! You can see the copy number alterations, gene expressions. Anyway, these papers will be coming out next week.

BRUG 25 Associates

Finally, to acknowledge people who did the work in my laboratory, Pena-Llopis. We have had a close collaboration with the people at Mayo Clinic, and also the group at Genentech. We also work very closely with our surgeon and Payal Kapur, our pathologist.

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Pathology and Why It is So Damn Important!

INTRO SLIDE

How Does the Pathology Report Help Direct my Treatment Options?

Lecture by Dr. Daniel Luthringer of Cedars Sinai Medical Center of Los Angeles at Kidney Cancer Association meeting December 2013. https://www.youtube.com/watch?v=-6emPs-mc1E   (Follow via YouTube)

I have transcribed the lecture edited for readability, included the slides, to make it easier to follow.  If you have not seen your own pathology, GET THAT REPORT now. Important to read!

A terrific introduction by Dr. Robert Figlin reminds us of the work of those people we never meet, but who care for us. “One of the people behind the scenes is the pathologist at this and other institutions. Often times the pathologist is in a different part of the hospital evaluating tissue, and helping the clinician figure out what the tissue looks like. It’s become, as Hyung (Dr. Kim) mentioned, time to start to think about personalized approaches to kidney cancer, and the relationship between the pathologist, the surgeon, and the clinician becomes ever more important. Dr. Daniel Luthringer is Professor of Pathology and Section Chief of the Genitourinary Pathology. He will talk to us about how the pathology report and how what he does– is important to then what we decide how to go forward with treatment.”

Dr. Luthringer begins:

“Thank you, Bob, for this introduction and the ability to speak at this conference. I am the guy behind the scenes, at least at this institution responsible for doing the histologic/microscopic analysis of genitourinary malignancies, primarily renal cell carcinomas. (RCC)

1 PATH 1 PathReportTypesThere are really two main categories of specimens we receive, samples from the real tumor itself, which can either be biopsies or resections, as Dr. Kim alluded to, or samples from a metastatic site, a recurrence or a metastatic site. The most common specimens that we see are nephrectomies, resections of the tumor, andeither partial nephrectomy or complete nephrectomy.

2Path 2 Types of Spec These are examples. A partial nephrectomy, as per Dr. Kim, are smaller resections or partial resections of the entire tumor.They include a bit of nephric fat and a little bit of the perinephretic fat as well. The goal is to get the entire tumor out, with a negative margin of resection. With tumors that are bigger generally, or infiltrative, we tend to get the entire kidney. This is an example of a nephrectomy with perinephric fat, the sinus fat, drainage area down here, maybe an adrenal gland up top and this would be an example of tumor that is completely resected.

Occasionally we will get tumors from metastatic sites or—unusually from the primary tumor—and will get a core biopsy, which is really a small smaller sample of the tumor mass. Usually it is about a millimeter or two in diameter; it’s a core, maybe up to several millimeters up to a centimeter in length. Generally, it is just a small sample of a much larger tumor .

Path 3 Speci Handling3  A bit about the specimen handling: within a few minutes of having the tissue removed, it comes to the pathology lab. We do some initial assessment on it.  We have work stations where they will come and the pathology team will assess it. Assume it is a nephrology specimen.  We look at it and measure it, cut it open, procure some of the tissue.  If there is some tissue that needs to be taken fresh, potentially for a biobank to be stored away, or if some tissue needs to be taken for immediate diagnosis or margins or something like that, we will do that.

If you’re enrolled in a study where there some fresh tissue is needed, sent to a particular institution or a reference laboratory for an analysis, we will procure that as well and make arrangements to send it off on an immediate basis. At that point we do photography, tissue fixation and over the next few hours we will dissect the specimen, will analyze it, do a lot important evaluation with our eyes and ears, whatever it takes. Then we will take what are called representative sections of that tumor or specimen, put them. We put them into these little capsules called cassettes and then we process them overnight in these tissue processors. These are pretty standard from institution to institution.

Path 3a Specimen Handling3a The next morning the tissue is taken out of the processors and is manually placed in these other tissue cassettes which are filled with paraffin wax essentially. They are embedded into these wax molds, and then the blocks. Then very thin sections of 4 to 5 microns are cut with these special microtomes and they are picked up on the glass slides. They are again processed, stained, and cover slipped. Ultimately we get a sample of glass slides from that tumor that has been removed.  On an average partial or complete nephrectomy, we will go anywhere from 5-10 paraffin blocks, equating to 5 -10 glass slides.

Path 4 Speci Handling2This takes about a day or two to complete this. Then the initial slides are delivered to the pathologist, who will begin the process of microscopic analysis. He uses obviously his microscope and whatever tools he needs.

He’ll be looking at those sections from the slides, and it will usually be the sections from the kidney, maybe some lymph nodes, margins, adrenal glands, things that were provided by the surgical resection. The whole process usually takes 2-3 days to complete. There is a bit of a time lag, due to the technical processing involved.

Path 4a Import element of report4a The Elements of the Report. Once we generate the report, and it becomes available, there are really three categories of information that are really relevant– not just the diagnosis, but the future care of the patient. The first is the diagnosis. What is the diagnosis? Is it really renal cell carcinoma or is it some other unusual type of renal cell cancer? I will talk more about that. Then: aspects related to cancer stage–tumor size, local infiltration. Has it metastasized or spread? Last, the other features that Dr. Kim alluded to in his talk—resection margins, grade, vascular invasions. We will talk to about these just briefly.

Path 4b Not all masses4bThe first aspect is diagnosis. The important thing to remember, and I think everyone in the room is a little bit beyond this, but remember that at the initial phase, tumors are resected and often times it is not know if it is a RCC. Often times it isn’t even know if it is a neoplasm at all. Not all tumor masses are neoplastic or malignancies.

Path 5 Exp of non cancer tumors 5 Examples of non-tumor masses would be like cysts, a lot of cysts. A lot like this or areas where the collecting system is dilated called hydronephrosis or multiple cysts can present or look just like a RCC. They are resected as if they were RCCs. But in fact they are not—they are benign

There are other types of tumors besides kRCCs. Angiomylipomas are a very common tumor. They could be very big like this one. Here’s a kidney. Here’s a big one. They could be multiple. Here’d two. They could be small one or 2 cm like this, but they all look like fatty tumors, but not all RCCs. Different types of tumor like fibroma or oncocytoma can be very big and aggressive-looking, but in fact, they’re not malignant at all.

Path 6 ex of cancer not RCC6 There are other types of malignancies, true malignancies of the kidney which are not real carcinomas. Urothelial tumors, those that are derived from the lining of the kidney that can extend into the kidney, be derived of the kidney. These are examples of some of these here. They were resected, thinking that these are probably RCCs, but in fact they turned to be urothelial, not RCCs.

Different types of tumors like sarcoma can be derived of the kidney or around the kidney. Other types of tumors can metastasize to the kidney or near the kidney. Adrenal tumors, lymphomas—there is a whole host of malignancies which can mimic RCC.

Path 7 RCC7 What were really talking about today here obviously is renal cell carcinomas which represent probably 90% of more of all true malignancies of the kidney. These are the tumors which are derived from the renal tubular epithelian cells, those little ducts that line the epithelium of the kidney. The diagnosis of RCC really is contingent upon microscopic analysis. You can’t make the diagnosis any other way.

The pathologist needs to look at the gross, take a section, look under the microscopic, and then there’s a spectrum, a range of features that will ensure the diagnosis or put it into a diagnostic category of RCC. Sometimes is not so simple. We need special testing–the use of antibodies, immunohistochemical studies or even as Dr. Young Kim alluded to, sometimes we need to refer to some molecular analysis to put it into a diagnostic category of RCC.

Path 7a RCC Subtypes7a Once we’ve done that, the next phrase is to determine the subtype. There are many different subtypes of RCCs really based primarily on the appearance of the tumor cells and their architectural growth patterns. Sometimes they can rely on immunohistochemical, some of the molecular properties or genetic profiles that put it in the proper subtype category.

Now the subclassification of RCCs and probably this is familiar. You’re familiar with RCCs and it is not so simple. It’s an evolving, sort of complex and ever-changing categorization. In fact, the overall categorization of subtypes just changed a few months ago. We like to think about RCC and subtypes in a sort of developmental pathway.

There is a sporadic type– that which just happened to occur–which is probably the type of cancer that most people in this room happen to have. Those are our typical clear cell, chromophobe, papillary renal cell carcinomas or maybe a few of the other rare variants.

There are those which tend to be familiar; these represent 90+ percent of all RCCs. The familial patterns–again what is associated—they are pretty rare. They are associated with and in families, multiple tumors. Different family members can have these, and we will talk a little bit more about these. There is actually going to be a talk about later in the afternoon or the morning about genetic-based or familial-based RCCs.

There are those rare—really associated with treatment of other types of cancers, and there is unusual category when you have scarred or damaged kidneys. Those kidneys are at risk for developing RCC.

Let’s move through this little bit. Once we have made the diagnosis of RCC, we’ve sub categorized it. I know it seems complex, but there are really only three or four main subtypes that we really need to talk about, especially in the context of a setting like this.

Path 8 RCC Most types8 The most common subtype is the clear cell type. This represents about the vast majority of all sporadic types of renal cell carcinoma. Then there are the papillary and chromophobe renal cell carcinomas. Since these are really the usual types. The much less common type is collecting duct carcinoma which is really more like a urothelial cancer, it behaves like a urothelial cancer, it’s a more aggressive type of RCC.

These are really the main four that we need to be concerned about. They are each unique based on their gross appearance and these are all partial nephrectomies (this is complete down here). Look at their gross appearance. They are very unique under the microscope. Look at their microscopic appearance.

The clear cell is clear, the papillary, very architectural pattern of a papillary tumor. These are chromophobe. This unusual eosinophilic cytoplasm are the tumor cells. Probably doesn’t mean a lot to you, but it means a lot to us, also to some other clinicians. So they have very characteristic gross, microscopic and they are very unique biochemical—and as Dr. Kim alluded to—very specific molecular and genetic profiles as well. This is all really evolving as we speak.

And we all know—this is small graph—that these also behave differently, Some behave better than others, so it is really important that we subclassify these RCCs based on their appearance—all the appearances that we talked about.

Path 9 Potential Therap Implic9 The other thing that Dr. Kim alluded to, and I think we are going to talk about this a little later, and I won’t get into detail on this, but just to point out that the sub-classifications, the sub-categories, they respond differently to the different armamentaria that we have in terms of treatment modalities. So it’s very important for the pathologist to sub classify the type of RCC.

Path 10 typ report10 So on any standard pathology report, you are going to see the diagnosis, RCC, then the subtype, buried somewhere in the report; It will say, clear cell type, papillary type, chromophobe. That’s a very important part of the report.

 

 

 

Path 11 Imp Elements of path11 After diagnosis, the next important aspect is the cancer stage; The cancer stage is really defined by the size of the tumor and its local growth. Is it extending, is it staying confined to the kidney, outside the kidney to the local fat, is it going into any regional lymph nodes that might have been removed during surgery, or was it extending into the adrenal gland, which might have been removed as well? So we analyze each case on what we have and what we see.

This is a typical example of a partial nephrectomy specimen of clear cell carcinoma with a margin that’s out here. Here it measures about 2.1 centimeters the margin is negative. This is a very small tumor of clear cell RCC. This would stage out at T1a, pretty low stage tumor. This would have a pretty good prognosis based on that staging profile.

Path 12 Imp elements of Path 212 Now compare that with this tumor which is a complete nephrectomy specimen, shown the kidney, a lot of nephritic fat. Here’s the sinus of the kidney and here’s the tumor out here. Much bigger, about 9 centimeters and it is growing into the fat. It’s growing into the sinus fat; it is demonstrating more aggressive local growth. This would stage out—this is a microscopic showing it extending into fat. We would stage this out at T3a tumor, as it is obviously larger and more infiltrative.

Path 13 Imp Elements313 A different example would be the same thing. A RCC clear cell type; this is a full nephrectomy specimen. Here’s the kidney. Notice that the tumor is extending into the renal vein. This is another feature that we analyze and look for. We look for it grossly and microscopically and look for tumor extension into that vein, because that will upstage the tumor, overall tumor stage, and this is associated with generally adverse outcome. It is telling us this tumor is behaving more aggressively with local growth. We might see a lymph node, with metastatic clear cell RCC. Again, another aspect we would examine grossly and microscopically.

Path 15 Import elemts 515 So we take all these features, once we have analyzed the tumor and we apply the grading system created by the Joint Council on Cancer Staging, the AJCC and we apply the pathologic stage. Why? Because as Dr. Kim alluded to, we all know, that cancer staging, and it is true for any type of cancer, the higher the stage, the more aggressive that tumor will likely behave therefore the therapy needs to be tailored to their particular stage. And the report should indicate clearly dictate the tumor stage. And that’s part of the standard reporting. Any good cancer report.

Path 14 Impor Elements 414 The final cancer features I’m going to talk about we’re talking about are; resection margin, the grade, vascular invasion, tumor necrosis and this this unusual rhabdoid or sarcomatoid differentiation. These are elements which go beyond cancer staging and the diagnosis. Here’s two examples.

Path 16 impor eleme616 Let us talk about resection margins. These are indirectly related to or they indicate the local aggressiveness of a tumor, if they are growing to a margin. It’s ideal when a partial nephrectomy or a complete nephrectomy is performed, as we have here, the surgeons always try to get the whole thing out so we achieve negative margins . That is optimal. Sometimes it’s not possible, especially if we have a high stage RCC like this one which is extending into fat. Sometimes it’s impossible to get a clear margin. This might get portend some additional therapy when it comes to therapeutic– time for a therapy . With a smaller resection sometimes it’s impossible to get a negative margin or the surgeon needs to go back and take cleaner margins. That interpreted for frozen section analysis, and clear out that margin, again because optimally, we want to achieve a negative resection margin.

Path 17 Imp elements 717 The next factor is vascular invasion. When the tumor invades into those lymphatics that Dr. Kim talked about in surgery. They have a propensity for them to go to the lymph node or they can go into veins or even sometimes arteries and then they have unfortunately, the capacity to go to the lungs or bones or other sites. Those confer an adverse prognostic indicator. Those are an indicator that this tumor might behave in a more aggressive manner. So if we see it microscopically, we include it in the report. Also if there’s tumor cell degeneration and necrosis, that is usually associated aggressive growth in the tumor and we will report that, too. Sometimes that will dictate how the next round of therapy will be undertaken.

Path 18 Imp elem 818 Dr. Kim already talked about tumor grade. We apply–the pathologist applies the tumor grade. The Fuhrman grade is the one that is used for RCC, and it a grading system for 1 to 4. Really, it delineates the degree of differentiation. Grade 1s are well-differentiated tumor, grade 4 are poorly differentiated and in any type of tumor–doesn’t matter if it’s breast, color, renal cell carcinoma–generally well-differentiated tumors behave better than poorly-differentiated tumors.And we assign a grade based on our observations.

Path 19 Imp Ele of report19  Finally, sarcomatoid or rhabdoid differentiation. Most tumors will have just one type of differentiation. This is an example of RCC. The vast majority are RCCclear cell, the conventional type. But in it, there were some pockets where the tumor cells had this unusual morphology under the microscope, called sarcomatoid differentiation, or over here, with we had this rhabdoid differentiation. You can see it that it’s very different than clear cell. These, for whatever reason, are associated with tumor aggressiveness. So when we see this, we need to report it. We need to quantitate it, and we put it in the report because these mandate some additional therapy, independent of stage, because they are really associated with aggressive tumors

All these last category features that I talked about, once we have observed them, we include them in the report. Again, usually any standard RCC report will have these features included in them because they will really impact upon therapy. *See slide10

Path 20 Hereditary20 Two quick categories and I will be done here.I was say a couple of words about hereditary genetic syndromes associated with RCC. This is taken out there that long list that I presented a few slides back. We all know that there are well-known, well-defined syndromes–genetic syndromes or familial syndromes that put you at increased risk from dying from other neoplasms, including RCC, notably Von Hippel Lindau, tuberous sclerosis, Birt-Hogg Dube, these sorts of things. The bottom line: as a pathologist, I can’t look at most of these tumors and say, “this is a clear cell carcinoma. It’s clearly Von Hippel-Lindau, tubersclerosis, or whatever.” All I can say is that it is clear cell carcinoma.

Path 21 Hereditary Genetic21 There are a few types of tumors that I can look at and say, if they have unusual morphology, like this tumor up here, or this tumor up here (references images) , they don’t comfortably fit into the typical types of RCC. Maybe it is a syndromic-type of carcinoma. Very, very rare, less than one percent that we would ever suggest to a clinician that maybe this is syndromic. What we can do is when we get samples like a renal resection like these three different cases, where there are multiple tumors. Here we have multiple tumors or multiple cysts—here we have maybe 20 or 30 different tumors in the particular kidney—or here’s a younger patient with one, two, three separate tumors. Then we can suggest that there is something odd about this, as we usually don’t see this in sporadic type tumors. Maybe it is associated with a genetic syndrome. So; multiple tumors, cysts, a young age, presentation of a renal cell carcinoma of unusual histology, we will suggest to your treatment team that maybe this is a genetic or syndromic pattern of RCC. There’s going to be more on this topic later this morning.

Path 22 Secondary Reviews22 The final topic I was asked to talk about the performance of secondary slide reviews. It’s kind of important. It’s really important when you come to an institution for definitive therapy, it’s always good to have that team—and we do this all the time—review the outside slides to be sure that you have an expert team who works with your treating physicians. We work as a team through tumor board reviews and discussions, and almost every discussions–.                                                                                                                                                       Almost every single individual case, to ensure that we have the correct diagnosis. We have the critical elements included in that report. The specific special testings have been performed, and we have accurate diagnosis and staging and things like that. What you need to do is provide, when you come here, is a copy of the reports, a set of the glass slides, sometimes we call them the recuts. That is all we need to provide an incoming secondary review.

The other scenario when you go off, you might need to off somewhere else for some additional testing for some additional therapy. In that situation, you might need to take, or you should take a set of slides with you to that institution because they will probably want to the same thing and review to ensure that we are all talking about the same disease process.

Remember that your slides or blocks, when you are treated here, or whatever institution, generally those tissue blocks are stored in an incredible huge file, either in the basement of the hospital right below us here or in a warehouse as we have done down in Torrance. T. They are basically saved forever. So when you need to go somewhere in five or ten or fifteen or twenty years, God forbid that there is a recurrence, and you need to get some additional testing, we can pull those blocks out from Torrance (CA) and create a second set of recuts, or a third or fourth set. We can send it off wherever it needs to go for some additional testing or evaluation.

Path 23 Authorizat23 What you need to do is fill out this authorization form here at Cedars if you are being treated here at Cedars. All you need to do is check off “Get a copy of the pathology report” and please provide a set or recut. It’ll take a few days, three days. We’ll get that for you, send it where it needs to go, or we can give it to you directly and you can just carry it with you to that next institution or wherever you need to go.”

With that Dr. Luthringer thanks the KCA, the audience and Dr. Figlin for the chance to speak.  And with that, I agree remind you to get a copy of your own pathology report, and know where your slides are stored. If there is any questions as to your own pathology, if the tumor seems to be unusual, or of an especially high grade, do yourself and your family a big favor, and discuss whether a review of your slides is in order!

With this rare disease, and the complexity of doing the kind of analysis you see here, do not be afraid to get that second opinion.  Go back and see so that pathology may affect the treatment options given–very important!

 

 

 

 

 

 

 

 

 

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Uniting the Genome & Clinic to Advance Care of Renal Cell Carcinoma: ccA & ccB –Lecture by Rathmell, MD, PhD

Why should you care about genomic research?  Simple; it could save your life! Want to know EXACTLY which type of cancer you have, and how to choose the best treatment?  New hope comes from this research which really examines the nature of the cells that make up your cancer.  Pretty important stuff.

  Genomic research is bringing improvements to care, and points up the need to be aware of this new knowledge–and if your own doctor is keeping up with that type of data. At a 2012 Conference sponsored by the The Oncology Journal, Dr. Kimrym Rathmell spoke in regard the genomic knowledge that is leading to improved care for kidney cancer patients. Maybe the most critical lecture of late.

Dr. Rathmell begins after introductory remarks; Complete access on YouTube via this link:

First, kidney cancer, like pancreatic cancer, has been on the rise. This is a somewhat dated slide, dating back to the 70s. We have seen a steady increase in this cancer. Although it was originally characterized as a rare tumor type, it is not really anymore.This talk will focus on one subtype of kidney cancer, that is, clear cell histology renal cell carcinoma. This is a histology slide showing why it is called clear cytoplasm

  1 Incidence of and Mortality of Kidney2 Focus on clear cell RCC

This tumor is characterized by particular mutation. That is the Von Hippel Landau gene, coordinate the loss of 3p, (a chromosome) where VHL is housed. We see these in mutations and loss of 3p which house other tumor suppressors as well, in up to 90% of these tumors. Based on this strong correlation between clear cell renal cell carcinoma and the VHL mutation, a tumor type. is a very distinct paradigm in which VHL loss causes upregulation of hypoxia inducible factors (HIF). These tumors are characterized by loss of high loss of these HIF factors. These are transcription factors that normally allow cells to respond to low levels of oxygen by turning on a repertoire of genes that allow them to bring in new blood vessels, to shift their metabolic properties, to migrate away, to promote survival, and to de-differentiate. That is a perfect storm for kidney cancer, in some respects.

3 Pathways of action Low o 2 VHL mutation4 Pathways with related agents                                               Targeted Agents in Use

Because this cancer has highly nonresponsive to typical chemotherapy, there’s much effort in recent years to develop targeted agents. These targeted agents to date all focus on this well-known pathway in clear cell type renal cell carcinoma. Most of the agents focus far down on this pathway, including that of receptors of VEGF and PDGF. They are tyrosine kinase inhibitors, effective at reducing the tumor angiogenic profile and can be quite effective at reducing the bulk of these diseases. Other drugs similarly target this pathway, for example, targeting features of the tumor that enable HIF to be stabilized such as that in the mTOR pathways.  Temsirolimus and Everolimus are approved for use. There are in-developments drugs for targeting MET, which is another mutation that can occur in this cancer, similarly increases HIF levels.

5 the reality of treating RCcBut the reality of treating kidney cancer is that the available drugs that we have do not produce complete responses. We only work in the arena of minimal response and partial response. The extent of response that a patient gets is unpredictable. The duration is also unpredictable and the toxicity is also unpredictable. For drugs we expect them to be effective on average 1 to 2 years, this is chronic therapy, very expensive, and it’s dominated by effects that are substantially detrimental to quality-of-life—fatigue, rash, diarrhea, as well as laboratory abnormalities that indicate damage to the liver or elevations of glucose and cholesterol.

PART I: Clear Cell Renal Cell Carcinoma, Molecular and Genetic Contributions to

INTER–Tumoral Heterogeneity.6 Renal Cell Carcinoma

With that, I will talk about various molecular probes that we use to understand some of the diversity or the heterogeneity of these tumors across the clear cell renal cell carcinoma spectrum. Before I really dive into clear cell  renal cell carcinoma, I need to point out that there are other histologies with this tumor as well. So when we say kidney cancer, we’re talking about a big spectrum. Clear cell renal cell carcinoma, we are talking about those tied to Von Hippel Lindau disease and loss of 3p and it is about 70% of all cases we encounter in cancers of the kidney. But there are also other types. Papillary type renal carcinoma, chromophobe, benign tumor—oncocytoma, a translocation form and some very rare. With these types of tumors we have very little in terms of knowledge of how to treat these patients.  Their genetics are highly distinct from clear cell renal cell carcinoma. So someday in the future, we will understand not only how to treat not only our clear cell carcinoma patients, but how to use effective molecular information to target these cancers as well.

7 ccRCc is well known to be molecuallry heteroge

Clear cell carcinoma is well know to be molecularly heterogeneous for some time. This is  a gene expression profile. We’ve already seen heat maps from several of these other talks, looking at gene expression profiles. And as you can see the gene expression profiles across a large selection of tumors here, suggests there are great areas of variability–at least two and as many as five groups, based upon gene expression purely.

8 Expression-directed pattern recognition Concensus cluster

                                                                        Pattern Recognition Profile to Find Subtypes

Our group undertook at the time developing a pattern recognition profile which is now fairly routine use. To try to see with a more robust computational strategy what subtypes we could really identify, that we could really pen down and understand with genetic profiles. 8aWe found two. For lack of better knowledge, we are calling clear cell A and clear cell B, ccA and ccB. These are very distinct biologically, and when we look at these tumors in terms of their outcome, they also have significant prognostic relevance–with the ccA tumors in this original cohort having a median survival of 103 months, compared to the 24 months for  ccB tumors.

9 Cancer Specific SurvivalThe TCGA which is been discussed here in many of the previous talks is a great source of validation. We assigned these tumors to clear cell A and cc B groups subtypes, validating our previous results with the clear cell A tumors having much better survival profile than those ccB tumors.

10 TCGA Validation, confrims prognostic valueThis classification scheme, which is based 120-130 gene signatures classified robust subdivisions of clear cell type renal cell can be applied with a small number of genes on individual tumors and is independently associated disease-specific overall survival, making it a valuable prognostic biomarker.

11 ccA, ccB RCc Classification

PART II: Rare Variant Groups12 Rare variant groups

We use these profile tools to understand the rare variants. This is still in the clear cell renal cell carcinoma arena, but when we took a very large group of compiled tumors; this was a meta-analysis of 500 tumors, all histologically defined as clear cell type renal cell carcinoma, and we applied our expression pattern recognition algorithm. We asked for two groups and we found two and they correlated with our ccA and ccB, but when we ask for three groups, we can find a small group that now filters out. Now that we have power in numbers to identify what we called Cluster 3.  What is in Cluster 3?

Cluster 3, as we’ve said, is histologically defined as clear cell renal cell carcinomas. But we look to the genetic expression profiles, it’s very different, particularly with regard to metabolic properties. We see upregulation of genes that are involved in mitochondrial regulation and oxidative phosphorylation, suggesting a striking difference in the way these tumors likely regulate metabolism.

 

13 What is in Cluster 3

14 Cluster 3 tumor display

In addition, and now these are tumors that we can not go back and genotype for VHL mutation, for loss of chromosome 3p, but the loss VHL regulation leads to  characteristic changes in the gene expression profile. So when we use the gene expression changes to predict whether these tumors have an intact VHL or a mutant type VHL. The wild type VHLS signature shown here is shown in  purple. You can see that these purple tumors, the wild type VHL tumors all tightly cluster with Cluster 3. These are probably not clear cell renal cell carcinomas although many, pathologists call them that. So we pulled them all out so, asking, “DO they look a little bit different?”  My graduate student, who did this work, came right away and said “There’s something funky about these clear cell tumors that we call Cluster 3.”

16 a New Paradims of subtypes for clinical stratificaiton15 Transcriptional segregation coincides with distinct morphology

As you can see, these are clear cell A and a clear cell B tumors, but they all have the clear cytoplasm and really, what we are seeing, is that they are not distinct histologically, although they are very different molecularly. And as I have shown, they have a very different prognostic outcome. The Cluster 3 tumors; although the cells themselves might have clear cell cytoplasm that gave them the clear cell histology designation, they have a very different pattern of organization—with a papillary type of feature. So what we think it would be identified as is a new rare variant of clear cell renal cell carcinoma.

Simultaneously another group of pathologists identified, that the pathologists call clear cell papillary carcinoma. That suggests that we need to take a very great care as we treat these patients.  What we have is clear cell type renal cell carcinoma, most of which are VHL-mutated, and we do have clear cell A and clear cell B. These are the tumors we should be treating with the drugs with identified, based on the effect of the pathway that is activated by loss of VHL.  But clear cell papillary renal cell carcinomas probably won’t react very well, as they are VHL-wild type.  Just like papillary renal cell carcinomas don’t react well either.

16a summaryRC types

To summarize this section, clear cell renal carcinoma can be separated into ccA and ccB groups, based on transcript profiling, but further clustering can identify highly biologically dissimilar subtypes within the clear cell group, and that subtyping can convey a biological distinction which is a valuable tool for prognostic evaluation, and a likely cause of poor responses to some therapy.

Part III; Using Clinical Trials to Understand Biological Relationships to Response to Therapy

As my title indicated,  we also refer to clinical trials to help us understand renal cell carcinoma a bit more. A clinical trial we completed some years ago, LCCC0603, was in neoadjuvant trial that looked at the treatment of renal tumors with sorafenib. Patients were identified as having renal tumor and underwent CT scans for basic size, description and PET scan, and then were treated with sorafenib. It is the first generation VEGF receptor tyrosine kinase inhibitor for 4 to 8 weeks, and then underwent post treatment CT scan, PET scan and a nephrectomy. We are going to look at radiographic indicators of response, rather than molecular indicators.17 LCCC0603- A Pilot Study of Radiogrph

18 Response to sorafenib

Waterfall Graph with Response at 30% as goal

First standard RECIST criteria do show that we do see partial responses.  Again, there were no complete responses. Many had subpartial or minimal or some partial responses. Their tumors shrank, but most did not meet the standard criteria of 30% decrease in one longest size. Some tumors actually grew.

Now what we realized as we looked at these tumors, is that we probably need new ways to describe response. The standard RECIST criterion response is just based on longest diameter and measuring this in comparison, after treatment..

I will use this patient is an example. (References I and J, in the lowest row). Here is a pretreatment; we have a very large renal tumor. Post treatment, the tumor was still large, but it measures slightly larger than it had been before.  But if you look at this tumor, it is very different. The central area of this tumor is now very dark, indicating necrosis—is what we think. But we took these tumors out, we could confirm that these dark areas were indeed necrotic. So we developed a new way to try to quantify the area of the tumor that is actually killed in response with this treatment.

14a Metabolic

19 new Ways to Measure Response

Similarly we were doing PET scans on these patients, and we were doing this because we’re trying to understand how the metabolic properties of these tumors might indicate how these tumors were likely to respond to this treatment. We see, and have known, that are some tumors which are very dim on FTG PET. This is a tumor; (Smallest of upper images) you can see that here is very visible on the PET scan. It doesn’t take up any FTG. So this tumor has the metabolic profile that is not dependent upon uptake of glucose. Others; this tumor (Smallest of lower picture), for example, have regional areas that are can be very high in terms of FTG uptake. When we looked at these tumors, we discovered first that non-clear histology tumors were much more likely to have high levels of FTG uptake. So, metabolically active tumors more likely in the (correction) non-clear cell group, probably the papillary, the chromophobes and the papillary clear cell types, than the clear cell group. Secondly. we discovered that the correlation between FTG uptake and response looked somewhat different than we might have expected. We might have expected the most metabolically active tumors would be those that would response better to anti-angiogenic agent. But the opposite was true. The best are those that had very low levels of uptake FTG uptake. We are still trying to understand exactly what that means. Certainly that means that those clear cell tumors are the ones more like to respond, activity, what we have known, but those are the ones with the lower level FTG activity.  But we continue to try the metabolic properties of the tumors that make theme different more likely to respond.

21 LCCC1028That leads to our next clinical trial. This is now ongoing. This is LCCC1028. It is a neoadjuvent clinical trial using the newest generation—well, they are  coming out so fast that it’s the not the newest, but the next to newest VEGF receptor tyrosine kinase inhibitor. They are now getting PET scans and a biopsy to confirm in fact that they would be clear cell renal cell carcinoma, and also to allow us to do molecular studies that directly measure their metabolic activity and other effects. They’re being treated for eight weeks with another CT scan, undergoing nephrectomy. We will then be able to look at clear cell variant histology. They will all be clear cell going in, but there may be variants included–as well as looking at their VHL mutation and their other mutational status, their transcript profile,  in particular  the clear cell A and clear cell B group and other protein expression signatures.

23 Genetic Intratumoral Heterogeneity22 What lies beneath the variatble historoloyg of human tumors-

This, of course, is known for all tumors, but if you sample in multiple different places, the histology will look different and in effect,  the grade can look different depending on where you are sample.

What does that mean molecularly? Well, a group at the Sanger Center published on a small number of tumors. When they sequenced these tumors, they found while there are some mutations that are ubiquitous, meaning the mutation is found in all samples across the primary tumor and the metastatic tumors, that there are mutations that are private.  There are mutations that are common only among the primary tumors and there are mutations that are common only in the metastases, and there are a lot mutations that are unique to the individual sample. This makes a whole new level of complication as we moved toward personalized therapy, in particular therapy that is based on biopsy metrics.24 Expression profiling in a heterogeneous tumor

This group also looked at our clear cell A and B subtypes. And what they saw, when they looked at six samples from the primary tumors, was  that in five of those samples, the gene signature indicated that these would be clear cell B type tumors. So depending  on  your glass half-full/glass half empty: The glass half full version of this, that  five out of six times, they would pick that the patient would have poor outcomes. This patient has metastatic disease, so it fact, that is true. The glass half empty would be that one out of six times, he would pick wrong. This patient would have been  indicated to have clear cell type A tumor, and you might have predicted that this patient would do well, when in fact that would be wrong. So what helps us understand the limitation of this test.  It also gives us the opportunity to understand a little bit more about these tumors.

25 Future- Uniting imaging

(Footnote reads: BRIC Funded Grants LCCC1213) So for the future, a trial (LCCC1213) that we have really just initiated is uniting some of these imaging observations we have made with genetics.

We are taking in patients. This is patient number one. Patient number two just has his MRI last week. and doing an MR in coordination with the PET scan so we can get the detailed look at these patients’ tissue perfusions, vascularity and the density of these tumors, as well as  regional areas at the FTG uptake and sample according to the map that is created by the imaging, as well as samples that are collected, based on what we see grossly in the tumor. Here  you can see a sample that we collected from a tumor region that is highly distinct from the  mostly more pale yellow regions of tumor.

This is just begun, so I cannot tell how well were going to get to correlate the gene expression and genetic underpinnings, and what we see in the tumor and what we see in the MR / PET.  But it will help us to move forward.

To summarize are multiple ways for RCC to diverge.  The subsets can enrich tumor sets for clinical and genetic features, and a multiplatform approach that with genetics, molecular biology and imaging techniques will give us man ways to tackle a surprisingly very heterogeneous disease.

26 SummaryQED

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