Advances in Cutaneous Molecular Medicine Supplement Clinical Expertise

To sustain the role of expert in cutaneous medicine, dermatologists and dermatopathologists must embrace the molecular advances in medicine, according to Dr. Pedram Gerami.

"For the vast majority of dermatologists and dermatopathologists trained in traditional clinical medicine, the sheer volume of newly identified gene mutations, chromosomal aberrations, and related molecular tests, even within a focused area of specialization, is truly overwhelming. As in many aspects of life, such rapid and transformative changes may be met with welcome or resistance," wrote Dr. Gerami, who was a guest editor of the December issue of Seminars in Cutaneous Medicine and Surgery, which focused on molecular medicine.

Rather than giving in to the common fear that new technological advancements may replace years of clinical training, it is important to recognize that these advances are meant to supplement – not replace – the clinical expertise of dermatologists and dermatopathologists (Sem. Cut. Med. Surg. 2012;31:203).

"The greatest threat to our practice is not the technologic advancement but rather loss of certain aspects of our practice to other specialties [that] better embrace the molecular revolution," he said, adding that active leadership with respect to integrating molecular medicine into the specialty will have a protective effect.

The first step is gaining a deeper understanding of these rapidly emerging advances. Among them are:

Diagnosis of Cutaneous Soft-Tissue Tumors

The identification of genetic abnormalities that characterize soft-tissue tumors has led to the development of diagnostic molecular testing, according to Dr. Alison L. Cheah and Dr. Steven D. Billings, both of the department of anatomic pathology at the Cleveland Clinic.

"Specific genetic signatures characterize a growing number of soft-tissue tumors that affect the skin. Molecular testing on FFPE [formalin-fixed paraffin-embedded tissue] complements histology and immunohistochemistry in the diagnosis of these tumors, especially in challenging cases with atypical morphology, nonspecific immunophenotype, and/or limited sampling," they wrote.

Molecular diagnostics also has implications for more accurate classification and prognostication of poorly understood entities (Sem. Cut. Med. Surg. 2012;31:221-33). "The identification of these disease-defining genetic signatures is the basis for the development of targeted therapies," they wrote.

Take dermatofibrosarcoma protuberans (DFSP), for example. "In practice, molecular testing in DFSP has utility both as a diagnostic aid in challenging cases and to guide therapy," they explained.

While most cases are easily diagnosed based on histopathologic features, significant diagnostic challenges can arise in certain cases, such as in CD34-negative tumors that are superficially sampled, or in tumors with varying histology or an unusual presentation.

For guiding treatment, molecular testing can be helpful for confirmation of COL1A1-PDGF-beta, which is vital if treatment with imatinib mesylate is being considered, because tumors lacking the fusion gene do not respond to this drug, they noted. Imatinib mesylate recently received Food and Drug Administration approval for the treatment of unresectable metastatic or recurrent DFSP.

Real-time polymerase chain reaction (RT-PCR) is the most studied test for detecting COL1A1-PDGF-beta and has a reported sensitivity between 74% and 96%. Though not as well studied, fluorescence in situ hybridization (FISH) assays also show promise.

"FISH assays using both PDGF-beta break-apart and COL1A1-PDGF-beta dual-color dual-fusion probe techniques have also been used," they wrote, noting that some reports show a greater sensitivity of FISH than RT-PCR for DFSP.

Molecular assays can also be helpful in confirming the diagnosis of angiomatoid fibrous histiocytoma (AFH).

In a study of 17 cases, FISH assays with dual-color break-apart probes had a sensitivity of 76% for identifying EWSR1 and FUS gene rearrangements, regardless of the translocation partner, they noted. FISH results should be interpreted with caution, though, because a negative result does not rule out the diagnosis of AFH, as rearrangements that are not detectable with the particular FISH probes used, or translocations with different chromosomes altogether, could explain a negative FISH result.

"Of note, EWSR1 rearrangements occur in several other soft tissue sarcomas, including Ewing sarcoma family of tumors, desmoplastic small round-cell tumors, clear cell sarcoma, extraskeletal myxoid chondrosarcoma, and a subset of myoepithelial tumors," they noted, adding that correlation with the histologic and immunohistochemical findings remains paramount.

RT-PCR is also a sensitive and specific assay for AFH, but its practical utility is limited by the multiple primers to account for the various fusion transcripts described in AFH.

Another area in which molecular testing plays an important role – albeit complementary– is in the diagnosis of low-grade fibromyxoid sarcoma (LGFMS), they reported. On the basis of RT-PCR results, for example, a significant number of cases previously diagnosed as LGMFS had to be reclassified.

RT-PCR assays performed on FFPE tissues had a sensitivity of 81%-88%, and FISH testing for FUS gene rearrangement is less sensitive at about 70%, but is nonetheless a good alternative to PCR, particularly in paraffin blocks with poor quality RNA.

These are just a few of the areas discussed by Dr. Cheah and Dr. Billings, with respect to molecular testing for cutaneous soft tissue tumors. Others addressed in their article were clear-cell sarcoma (melanoma of the soft parts), postradiation angiosarcoma, epithelioid hemangioendothelioma, and Ewing sarcoma family of tumors.

Knowledge and identification of the recurrent molecular aberrations in these cutaneous mesenchymal tumors allow for more accurate diagnosis and advancement of understanding about their underlying biology.

BRAF V600E Mutation Detection

The identification of BRAF mutations in the mitogen-activated protein kinase pathway revolutionized the treatment of advanced-stage melanoma, bringing selective small-molecule RAF inhibitors, such as vemurafenib, to the clinical trial stage. In the phase III BRIM-3 trial, vemurafenib was associated with a higher response rate and a significant improvement in survival, compared with dacarbazine.

"The knowledge that melanomas harbor recurring hot spot mutations in the BRAF gene has rapidly brought molecular testing to the clinical stage," wrote Dr. Jonathan L. Curry of the department of pathology at the University of Texas MD Anderson Cancer Center, Houston, and his colleagues.

The cobas 4800 BRAF V600 Mutation Test from Roche, for example, was approved by the FDA as an in vitro diagnostic device to detect mutant BRAF V600E in DNA extracted from a FFPE patient’s sample of melanoma (Sem. Cut. Med. Surg. 2012;31:268-74). The presence of the mutation aids in selecting patients for treatment with vemurafenib.

The authors noted that a number of molecular platforms for BRAF testing have been developed and continue to evolve, offering a more thorough and complex analysis of the genetic components of melanoma.

"The next generation sequencing or massively parallel sequencing will allow sequencing of the entire exon or whole genome. Multiple sequencing molecular platforms are available to examine for BRAF mutations in cutaneous melanoma, and the best technological approach continues to be developed," they wrote.

Among those they described are:

• Sanger Sequencing. Sanger chain–termination sequencing of amplified DNA by PCR was the method used to sequence the human genome, and the Sanger method of sequencing led to the detection of BRAF mutations in cutaneous melanoma. Sensitivity is high (fewer than 5% of tumor cells are necessary in a given specimen), but use in the clinical setting is limited to BRAF testing. Although it remains the gold standard for gene sequencing, the Sanger method has technical and practical limitations. For example, it takes 18-19 hours to perform the test, other tests are more sensitive, and it cannot detect changes in the chromosomal copy number and the translocations.

• Pyrosequencing. Also known as sequencing by synthesis, pyrosequencing is among the platforms more sensitive than Sanger sequencing. The detection ratio of mutant BRAF V600E to wild type is 1:5 for Sanger sequencing, and 1:50 for pyrosequencing. Its clinical application is to detect the presence or absence of known mutations within a specific segment of DNA of a single nucleotide polymorphism.

"Because mutations in melanoma appear to cluster in the BRAF, NRAS, and KIT genes, this molecular platform has been readily incorporated into the mutational analysis of melanoma," the authors explained, noting that pyrosequencing is a rapid and sensitive test for detection of more common BRAF V600E mutations, as well as other variants. It is limited to the length of the DNA template sequenced, and is prone to errors reading through homopolymer sequences.

• Allele-Specific Real-Time PCR. This molecular platform, also known as the amplification-refractory mutation system, enriches known mutations in clinical samples to increase sensitivity of detection, and is particularly useful in FFPE biopsies with low tumor content. It is highly sensitive and is confined to known BRAF mutations that occur in melanomas, but demonstrates greater sensitivity in detecting BRAF V600E mutations in FFPE clinical samples.

• Mass Spectrometry–Based Sequencing (Sequenom). Sequenom uses mass spectrometry to determine the sequence of the FFPE tissue samples of melanoma. The platform allows for simultaneous amplification of multiple genetic hot spots, allowing for analysis of several known mutations in a single clinical sample. In the authors’ experience, it has slightly higher sensitivity than pyrosequencing.

• High Resolution Melting (HRM). Also a highly sensitive method for screening for mutations in clinical samples, high-resolution melting relies on PCR amplification of the DNA template and analysis of the temperature gradient in which the double strands of the PCR products are melted. The strands melt at different temperatures, depending on the sequence of the constituent bases, allowing for detection of the mutant allele in the FFPE tissue sample. An important limitation of this approach is that specific nucleotide alteration is not reported, thus tissues samples that are positive for mutations will require additional sequencing by another method to determine the specific nucleotide alteration.

• The 454 Pyrosequencing (Roche). This powerful platform, one of several next generation sequencing technologies that allows ultra deep sequencing of entire exons, was used to resolve mutation discrepancies between the cobas 4800 BRAF V600 test and the Sanger sequencing method during the vemurafenib trials, the authors noted. It has a mean error rate of only 1.07%, with more than half of the errors at sites of homopolymers, has the lengths of individual reads of DNA sequences of more than 500 base pairs, and can be performed in less than a day.

• Cobas 4800 BRAF V600 Mutation Test. The cobas 4800 BRAF V600 Mutation Test is based on the principles of allele-specific real time PCR, and targets a predefined 116-base pair sequence of the BRAF gene on exon 15. The device, which is intended to identify those with BRAF V600E who might benefit from therapy with vemurafenib, has a sensitivity for detecting BRAF V600E on FFPE samples of melanoma of more than 99%, and a specificity of 88%. The sensitivity appears comparable with the other platforms, including Sequenom and HRM.

Although the platform is not designed to screen for nonrecurrent genetic mutations in melanoma, BRAF V600E appears to account for the highest percentage of mutations in cutaneous melanomas, the authors said.

Cutaneous Lymphoma Analysis

In cutaneous lymphomas, molecular analysis serves to confirm the diagnosis in cases in which the clinical and/or pathologic presentations do not provide a diagnosis and to further characterize the nature of the lymphoma, according to Dr. Janyana M.D. Deonizio and Dr. Joan Guitart.

While the gold standard for diagnosis is a solid clinicopathologic correlation, molecular analysis provides for a more concrete diagnosis that helps both the patient in facing the diagnosis, and the clinician in proceeding with the most appropriate treatment plan (Sem. Cut. Med. Surg. 2012;31:234-40).

Specifically, through immunophenotyping and clonality analysis, molecular analysis helps discern whether the lymphoma is primarily cutaneous or systemic with secondary skin involvement, and it subclassifies the tumor.

Methods for establishing T-cell clonality include Southern blot analysis (SBA) and PCR for detection of specific T-cell receptor gene arrangements (TCR-GR). SBA used to be the gold standard, but has been gradually replaced by PCR techniques which are less laborious and lengthy. PCR sensitivity for T-cell clonality detection ranges from 70% to 90%.

"Ideally, TCR clonality should be checked at the time of diagnosis in skin and blood. ... The detection of a dominant clone is important not only to confirm diagnosis but also for some prognostic guidance," they wrote, explaining that T-cell cloning is particularly helpful when early-stage mycosis fungoides is being considered in the differential diagnosis.

It does have limitations, however. False-positive monoclonal or oligoclonal bands may be identified in inflammatory dermatoses when T-cell infiltrates are sparse, resulting in "pseudomonoclonality," which is infrequently associated with a malignant T-cell process, they noted.

"Repeating the analysis using the same DNA template or fresh DNA extraction may solve the problem because in reactive conditions, the predominant PCR products typically vary in repeated PCR analyses of the same sample. In contrast, in neoplastic T-cell proliferations, dominant TCR clones are reproducible and should be routinely verified to confirm monoclonality," they noted.

Some studies suggest a correlation between TCR clonality by PCR and response to treatment; the absence of a detectable clone in cutaneous T-cell lymphoma (CTCL) has been associated with a higher rate of complete remission – although not necessarily with improved survival.

Immunophenotypic and immunogenotypic assays have been used to monitor the response of CTCL to therapy, define remission, and detect early relapse, thereby improving assessment of disease activity.

Flow cytometry analysis, for example, is "an efficient and sensitive method to detect and enumerate abnormal cells in the peripheral blood or any other cell suspension," they wrote. It can also be performed on leukocyte suspension from skin biopsies, and it provides prognostic information.

"Lower counts of circulating CD8+ lymphocytes and higher white cell counts in CTCL patients are associated with a less favorable prognosis," the authors noted.

FISH is used to detect major chromosomal gains or losses and specific translocations using a target-specific probe. Although FISH is not routinely used in the diagnosis of cutaneous lymphomas, it does appear to have potential future applications in various areas, according to recent publications.

Finally, genomic analysis by microarray-based comparative genomic hybridization is allowing quantification and appositional defining of chromosomal imbalances. While still confined to the research arena, this technology is providing some insight into the molecular pathogenesis of CTCL, the reported.

The advances in molecular diagnostics that are outlined in this series of articles are not limited to skin cancers and tumors. Additional articles, for example, addressed the role of genetic and molecular analysis in alopecia and in genodermatoses. Together they underscore the need for, and substantiate the ability of the specialty to take on leadership roles in molecular medicine, noted Dr. Gerami, of the department of dermatology at Northwestern University in Chicago.

"I am hopeful that they can assist other practicing dermatologists and dermatopathologists acquire a better foundation in molecular medicine, allowing them to sustain their primary roles in cutaneous medicine," Dr. Gerami concluded.

The authors reported having no conflicts of interest.

To sustain the role of expert in cutaneous medicine, dermatologists and dermatopathologists must embrace the molecular advances in medicine, according to Dr. Pedram Gerami.

"For the vast majority of dermatologists and dermatopathologists trained in traditional clinical medicine, the sheer volume of newly identified gene mutations, chromosomal aberrations, and related molecular tests, even within a focused area of specialization, is truly overwhelming. As in many aspects of life, such rapid and transformative changes may be met with welcome or resistance," wrote Dr. Gerami, who was a guest editor of the December issue of Seminars in Cutaneous Medicine and Surgery, which focused on molecular medicine.

Rather than giving in to the common fear that new technological advancements may replace years of clinical training, it is important to recognize that these advances are meant to supplement – not replace – the clinical expertise of dermatologists and dermatopathologists (Sem. Cut. Med. Surg. 2012;31:203).

"The greatest threat to our practice is not the technologic advancement but rather loss of certain aspects of our practice to other specialties [that] better embrace the molecular revolution," he said, adding that active leadership with respect to integrating molecular medicine into the specialty will have a protective effect.

The first step is gaining a deeper understanding of these rapidly emerging advances. Among them are:

Diagnosis of Cutaneous Soft-Tissue Tumors

The identification of genetic abnormalities that characterize soft-tissue tumors has led to the development of diagnostic molecular testing, according to Dr. Alison L. Cheah and Dr. Steven D. Billings, both of the department of anatomic pathology at the Cleveland Clinic.

"Specific genetic signatures characterize a growing number of soft-tissue tumors that affect the skin. Molecular testing on FFPE [formalin-fixed paraffin-embedded tissue] complements histology and immunohistochemistry in the diagnosis of these tumors, especially in challenging cases with atypical morphology, nonspecific immunophenotype, and/or limited sampling," they wrote.

Molecular diagnostics also has implications for more accurate classification and prognostication of poorly understood entities (Sem. Cut. Med. Surg. 2012;31:221-33). "The identification of these disease-defining genetic signatures is the basis for the development of targeted therapies," they wrote.

Take dermatofibrosarcoma protuberans (DFSP), for example. "In practice, molecular testing in DFSP has utility both as a diagnostic aid in challenging cases and to guide therapy," they explained.

While most cases are easily diagnosed based on histopathologic features, significant diagnostic challenges can arise in certain cases, such as in CD34-negative tumors that are superficially sampled, or in tumors with varying histology or an unusual presentation.

For guiding treatment, molecular testing can be helpful for confirmation of COL1A1-PDGF-beta, which is vital if treatment with imatinib mesylate is being considered, because tumors lacking the fusion gene do not respond to this drug, they noted. Imatinib mesylate recently received Food and Drug Administration approval for the treatment of unresectable metastatic or recurrent DFSP.

Real-time polymerase chain reaction (RT-PCR) is the most studied test for detecting COL1A1-PDGF-beta and has a reported sensitivity between 74% and 96%. Though not as well studied, fluorescence in situ hybridization (FISH) assays also show promise.

"FISH assays using both PDGF-beta break-apart and COL1A1-PDGF-beta dual-color dual-fusion probe techniques have also been used," they wrote, noting that some reports show a greater sensitivity of FISH than RT-PCR for DFSP.

Molecular assays can also be helpful in confirming the diagnosis of angiomatoid fibrous histiocytoma (AFH).

In a study of 17 cases, FISH assays with dual-color break-apart probes had a sensitivity of 76% for identifying EWSR1 and FUS gene rearrangements, regardless of the translocation partner, they noted. FISH results should be interpreted with caution, though, because a negative result does not rule out the diagnosis of AFH, as rearrangements that are not detectable with the particular FISH probes used, or translocations with different chromosomes altogether, could explain a negative FISH result.

"Of note, EWSR1 rearrangements occur in several other soft tissue sarcomas, including Ewing sarcoma family of tumors, desmoplastic small round-cell tumors, clear cell sarcoma, extraskeletal myxoid chondrosarcoma, and a subset of myoepithelial tumors," they noted, adding that correlation with the histologic and immunohistochemical findings remains paramount.

RT-PCR is also a sensitive and specific assay for AFH, but its practical utility is limited by the multiple primers to account for the various fusion transcripts described in AFH.

Another area in which molecular testing plays an important role – albeit complementary– is in the diagnosis of low-grade fibromyxoid sarcoma (LGFMS), they reported. On the basis of RT-PCR results, for example, a significant number of cases previously diagnosed as LGMFS had to be reclassified.

RT-PCR assays performed on FFPE tissues had a sensitivity of 81%-88%, and FISH testing for FUS gene rearrangement is less sensitive at about 70%, but is nonetheless a good alternative to PCR, particularly in paraffin blocks with poor quality RNA.

These are just a few of the areas discussed by Dr. Cheah and Dr. Billings, with respect to molecular testing for cutaneous soft tissue tumors. Others addressed in their article were clear-cell sarcoma (melanoma of the soft parts), postradiation angiosarcoma, epithelioid hemangioendothelioma, and Ewing sarcoma family of tumors.

Knowledge and identification of the recurrent molecular aberrations in these cutaneous mesenchymal tumors allow for more accurate diagnosis and advancement of understanding about their underlying biology.

BRAF V600E Mutation Detection

The identification of BRAF mutations in the mitogen-activated protein kinase pathway revolutionized the treatment of advanced-stage melanoma, bringing selective small-molecule RAF inhibitors, such as vemurafenib, to the clinical trial stage. In the phase III BRIM-3 trial, vemurafenib was associated with a higher response rate and a significant improvement in survival, compared with dacarbazine.

"The knowledge that melanomas harbor recurring hot spot mutations in the BRAF gene has rapidly brought molecular testing to the clinical stage," wrote Dr. Jonathan L. Curry of the department of pathology at the University of Texas MD Anderson Cancer Center, Houston, and his colleagues.

The cobas 4800 BRAF V600 Mutation Test from Roche, for example, was approved by the FDA as an in vitro diagnostic device to detect mutant BRAF V600E in DNA extracted from a FFPE patient’s sample of melanoma (Sem. Cut. Med. Surg. 2012;31:268-74). The presence of the mutation aids in selecting patients for treatment with vemurafenib.

The authors noted that a number of molecular platforms for BRAF testing have been developed and continue to evolve, offering a more thorough and complex analysis of the genetic components of melanoma.

"The next generation sequencing or massively parallel sequencing will allow sequencing of the entire exon or whole genome. Multiple sequencing molecular platforms are available to examine for BRAF mutations in cutaneous melanoma, and the best technological approach continues to be developed," they wrote.

Among those they described are:

• Sanger Sequencing. Sanger chain–termination sequencing of amplified DNA by PCR was the method used to sequence the human genome, and the Sanger method of sequencing led to the detection of BRAF mutations in cutaneous melanoma. Sensitivity is high (fewer than 5% of tumor cells are necessary in a given specimen), but use in the clinical setting is limited to BRAF testing. Although it remains the gold standard for gene sequencing, the Sanger method has technical and practical limitations. For example, it takes 18-19 hours to perform the test, other tests are more sensitive, and it cannot detect changes in the chromosomal copy number and the translocations.

• Pyrosequencing. Also known as sequencing by synthesis, pyrosequencing is among the platforms more sensitive than Sanger sequencing. The detection ratio of mutant BRAF V600E to wild type is 1:5 for Sanger sequencing, and 1:50 for pyrosequencing. Its clinical application is to detect the presence or absence of known mutations within a specific segment of DNA of a single nucleotide polymorphism.

"Because mutations in melanoma appear to cluster in the BRAF, NRAS, and KIT genes, this molecular platform has been readily incorporated into the mutational analysis of melanoma," the authors explained, noting that pyrosequencing is a rapid and sensitive test for detection of more common BRAF V600E mutations, as well as other variants. It is limited to the length of the DNA template sequenced, and is prone to errors reading through homopolymer sequences.

• Allele-Specific Real-Time PCR. This molecular platform, also known as the amplification-refractory mutation system, enriches known mutations in clinical samples to increase sensitivity of detection, and is particularly useful in FFPE biopsies with low tumor content. It is highly sensitive and is confined to known BRAF mutations that occur in melanomas, but demonstrates greater sensitivity in detecting BRAF V600E mutations in FFPE clinical samples.

• Mass Spectrometry–Based Sequencing (Sequenom). Sequenom uses mass spectrometry to determine the sequence of the FFPE tissue samples of melanoma. The platform allows for simultaneous amplification of multiple genetic hot spots, allowing for analysis of several known mutations in a single clinical sample. In the authors’ experience, it has slightly higher sensitivity than pyrosequencing.

• High Resolution Melting (HRM). Also a highly sensitive method for screening for mutations in clinical samples, high-resolution melting relies on PCR amplification of the DNA template and analysis of the temperature gradient in which the double strands of the PCR products are melted. The strands melt at different temperatures, depending on the sequence of the constituent bases, allowing for detection of the mutant allele in the FFPE tissue sample. An important limitation of this approach is that specific nucleotide alteration is not reported, thus tissues samples that are positive for mutations will require additional sequencing by another method to determine the specific nucleotide alteration.

• The 454 Pyrosequencing (Roche). This powerful platform, one of several next generation sequencing technologies that allows ultra deep sequencing of entire exons, was used to resolve mutation discrepancies between the cobas 4800 BRAF V600 test and the Sanger sequencing method during the vemurafenib trials, the authors noted. It has a mean error rate of only 1.07%, with more than half of the errors at sites of homopolymers, has the lengths of individual reads of DNA sequences of more than 500 base pairs, and can be performed in less than a day.

• Cobas 4800 BRAF V600 Mutation Test. The cobas 4800 BRAF V600 Mutation Test is based on the principles of allele-specific real time PCR, and targets a predefined 116-base pair sequence of the BRAF gene on exon 15. The device, which is intended to identify those with BRAF V600E who might benefit from therapy with vemurafenib, has a sensitivity for detecting BRAF V600E on FFPE samples of melanoma of more than 99%, and a specificity of 88%. The sensitivity appears comparable with the other platforms, including Sequenom and HRM.

Although the platform is not designed to screen for nonrecurrent genetic mutations in melanoma, BRAF V600E appears to account for the highest percentage of mutations in cutaneous melanomas, the authors said.

Cutaneous Lymphoma Analysis

In cutaneous lymphomas, molecular analysis serves to confirm the diagnosis in cases in which the clinical and/or pathologic presentations do not provide a diagnosis and to further characterize the nature of the lymphoma, according to Dr. Janyana M.D. Deonizio and Dr. Joan Guitart.

While the gold standard for diagnosis is a solid clinicopathologic correlation, molecular analysis provides for a more concrete diagnosis that helps both the patient in facing the diagnosis, and the clinician in proceeding with the most appropriate treatment plan (Sem. Cut. Med. Surg. 2012;31:234-40).

Specifically, through immunophenotyping and clonality analysis, molecular analysis helps discern whether the lymphoma is primarily cutaneous or systemic with secondary skin involvement, and it subclassifies the tumor.

Methods for establishing T-cell clonality include Southern blot analysis (SBA) and PCR for detection of specific T-cell receptor gene arrangements (TCR-GR). SBA used to be the gold standard, but has been gradually replaced by PCR techniques which are less laborious and lengthy. PCR sensitivity for T-cell clonality detection ranges from 70% to 90%.

"Ideally, TCR clonality should be checked at the time of diagnosis in skin and blood. ... The detection of a dominant clone is important not only to confirm diagnosis but also for some prognostic guidance," they wrote, explaining that T-cell cloning is particularly helpful when early-stage mycosis fungoides is being considered in the differential diagnosis.

It does have limitations, however. False-positive monoclonal or oligoclonal bands may be identified in inflammatory dermatoses when T-cell infiltrates are sparse, resulting in "pseudomonoclonality," which is infrequently associated with a malignant T-cell process, they noted.

"Repeating the analysis using the same DNA template or fresh DNA extraction may solve the problem because in reactive conditions, the predominant PCR products typically vary in repeated PCR analyses of the same sample. In contrast, in neoplastic T-cell proliferations, dominant TCR clones are reproducible and should be routinely verified to confirm monoclonality," they noted.

Some studies suggest a correlation between TCR clonality by PCR and response to treatment; the absence of a detectable clone in cutaneous T-cell lymphoma (CTCL) has been associated with a higher rate of complete remission – although not necessarily with improved survival.

Immunophenotypic and immunogenotypic assays have been used to monitor the response of CTCL to therapy, define remission, and detect early relapse, thereby improving assessment of disease activity.

Flow cytometry analysis, for example, is "an efficient and sensitive method to detect and enumerate abnormal cells in the peripheral blood or any other cell suspension," they wrote. It can also be performed on leukocyte suspension from skin biopsies, and it provides prognostic information.

"Lower counts of circulating CD8+ lymphocytes and higher white cell counts in CTCL patients are associated with a less favorable prognosis," the authors noted.

FISH is used to detect major chromosomal gains or losses and specific translocations using a target-specific probe. Although FISH is not routinely used in the diagnosis of cutaneous lymphomas, it does appear to have potential future applications in various areas, according to recent publications.

Finally, genomic analysis by microarray-based comparative genomic hybridization is allowing quantification and appositional defining of chromosomal imbalances. While still confined to the research arena, this technology is providing some insight into the molecular pathogenesis of CTCL, the reported.

The advances in molecular diagnostics that are outlined in this series of articles are not limited to skin cancers and tumors. Additional articles, for example, addressed the role of genetic and molecular analysis in alopecia and in genodermatoses. Together they underscore the need for, and substantiate the ability of the specialty to take on leadership roles in molecular medicine, noted Dr. Gerami, of the department of dermatology at Northwestern University in Chicago.

"I am hopeful that they can assist other practicing dermatologists and dermatopathologists acquire a better foundation in molecular medicine, allowing them to sustain their primary roles in cutaneous medicine," Dr. Gerami concluded.

The authors reported having no conflicts of interest.

To sustain the role of expert in cutaneous medicine, dermatologists and dermatopathologists must embrace the molecular advances in medicine, according to Dr. Pedram Gerami.

"For the vast majority of dermatologists and dermatopathologists trained in traditional clinical medicine, the sheer volume of newly identified gene mutations, chromosomal aberrations, and related molecular tests, even within a focused area of specialization, is truly overwhelming. As in many aspects of life, such rapid and transformative changes may be met with welcome or resistance," wrote Dr. Gerami, who was a guest editor of the December issue of Seminars in Cutaneous Medicine and Surgery, which focused on molecular medicine.

Rather than giving in to the common fear that new technological advancements may replace years of clinical training, it is important to recognize that these advances are meant to supplement – not replace – the clinical expertise of dermatologists and dermatopathologists (Sem. Cut. Med. Surg. 2012;31:203).

"The greatest threat to our practice is not the technologic advancement but rather loss of certain aspects of our practice to other specialties [that] better embrace the molecular revolution," he said, adding that active leadership with respect to integrating molecular medicine into the specialty will have a protective effect.

The first step is gaining a deeper understanding of these rapidly emerging advances. Among them are:

Diagnosis of Cutaneous Soft-Tissue Tumors

The identification of genetic abnormalities that characterize soft-tissue tumors has led to the development of diagnostic molecular testing, according to Dr. Alison L. Cheah and Dr. Steven D. Billings, both of the department of anatomic pathology at the Cleveland Clinic.

"Specific genetic signatures characterize a growing number of soft-tissue tumors that affect the skin. Molecular testing on FFPE [formalin-fixed paraffin-embedded tissue] complements histology and immunohistochemistry in the diagnosis of these tumors, especially in challenging cases with atypical morphology, nonspecific immunophenotype, and/or limited sampling," they wrote.

Molecular diagnostics also has implications for more accurate classification and prognostication of poorly understood entities (Sem. Cut. Med. Surg. 2012;31:221-33). "The identification of these disease-defining genetic signatures is the basis for the development of targeted therapies," they wrote.

Take dermatofibrosarcoma protuberans (DFSP), for example. "In practice, molecular testing in DFSP has utility both as a diagnostic aid in challenging cases and to guide therapy," they explained.

While most cases are easily diagnosed based on histopathologic features, significant diagnostic challenges can arise in certain cases, such as in CD34-negative tumors that are superficially sampled, or in tumors with varying histology or an unusual presentation.

For guiding treatment, molecular testing can be helpful for confirmation of COL1A1-PDGF-beta, which is vital if treatment with imatinib mesylate is being considered, because tumors lacking the fusion gene do not respond to this drug, they noted. Imatinib mesylate recently received Food and Drug Administration approval for the treatment of unresectable metastatic or recurrent DFSP.

Real-time polymerase chain reaction (RT-PCR) is the most studied test for detecting COL1A1-PDGF-beta and has a reported sensitivity between 74% and 96%. Though not as well studied, fluorescence in situ hybridization (FISH) assays also show promise.

"FISH assays using both PDGF-beta break-apart and COL1A1-PDGF-beta dual-color dual-fusion probe techniques have also been used," they wrote, noting that some reports show a greater sensitivity of FISH than RT-PCR for DFSP.

Molecular assays can also be helpful in confirming the diagnosis of angiomatoid fibrous histiocytoma (AFH).

In a study of 17 cases, FISH assays with dual-color break-apart probes had a sensitivity of 76% for identifying EWSR1 and FUS gene rearrangements, regardless of the translocation partner, they noted. FISH results should be interpreted with caution, though, because a negative result does not rule out the diagnosis of AFH, as rearrangements that are not detectable with the particular FISH probes used, or translocations with different chromosomes altogether, could explain a negative FISH result.

"Of note, EWSR1 rearrangements occur in several other soft tissue sarcomas, including Ewing sarcoma family of tumors, desmoplastic small round-cell tumors, clear cell sarcoma, extraskeletal myxoid chondrosarcoma, and a subset of myoepithelial tumors," they noted, adding that correlation with the histologic and immunohistochemical findings remains paramount.

RT-PCR is also a sensitive and specific assay for AFH, but its practical utility is limited by the multiple primers to account for the various fusion transcripts described in AFH.

Another area in which molecular testing plays an important role – albeit complementary– is in the diagnosis of low-grade fibromyxoid sarcoma (LGFMS), they reported. On the basis of RT-PCR results, for example, a significant number of cases previously diagnosed as LGMFS had to be reclassified.

RT-PCR assays performed on FFPE tissues had a sensitivity of 81%-88%, and FISH testing for FUS gene rearrangement is less sensitive at about 70%, but is nonetheless a good alternative to PCR, particularly in paraffin blocks with poor quality RNA.

These are just a few of the areas discussed by Dr. Cheah and Dr. Billings, with respect to molecular testing for cutaneous soft tissue tumors. Others addressed in their article were clear-cell sarcoma (melanoma of the soft parts), postradiation angiosarcoma, epithelioid hemangioendothelioma, and Ewing sarcoma family of tumors.

Knowledge and identification of the recurrent molecular aberrations in these cutaneous mesenchymal tumors allow for more accurate diagnosis and advancement of understanding about their underlying biology.

BRAF V600E Mutation Detection

The identification of BRAF mutations in the mitogen-activated protein kinase pathway revolutionized the treatment of advanced-stage melanoma, bringing selective small-molecule RAF inhibitors, such as vemurafenib, to the clinical trial stage. In the phase III BRIM-3 trial, vemurafenib was associated with a higher response rate and a significant improvement in survival, compared with dacarbazine.

"The knowledge that melanomas harbor recurring hot spot mutations in the BRAF gene has rapidly brought molecular testing to the clinical stage," wrote Dr. Jonathan L. Curry of the department of pathology at the University of Texas MD Anderson Cancer Center, Houston, and his colleagues.

The cobas 4800 BRAF V600 Mutation Test from Roche, for example, was approved by the FDA as an in vitro diagnostic device to detect mutant BRAF V600E in DNA extracted from a FFPE patient’s sample of melanoma (Sem. Cut. Med. Surg. 2012;31:268-74). The presence of the mutation aids in selecting patients for treatment with vemurafenib.

The authors noted that a number of molecular platforms for BRAF testing have been developed and continue to evolve, offering a more thorough and complex analysis of the genetic components of melanoma.

"The next generation sequencing or massively parallel sequencing will allow sequencing of the entire exon or whole genome. Multiple sequencing molecular platforms are available to examine for BRAF mutations in cutaneous melanoma, and the best technological approach continues to be developed," they wrote.

Among those they described are:

• Sanger Sequencing. Sanger chain–termination sequencing of amplified DNA by PCR was the method used to sequence the human genome, and the Sanger method of sequencing led to the detection of BRAF mutations in cutaneous melanoma. Sensitivity is high (fewer than 5% of tumor cells are necessary in a given specimen), but use in the clinical setting is limited to BRAF testing. Although it remains the gold standard for gene sequencing, the Sanger method has technical and practical limitations. For example, it takes 18-19 hours to perform the test, other tests are more sensitive, and it cannot detect changes in the chromosomal copy number and the translocations.

• Pyrosequencing. Also known as sequencing by synthesis, pyrosequencing is among the platforms more sensitive than Sanger sequencing. The detection ratio of mutant BRAF V600E to wild type is 1:5 for Sanger sequencing, and 1:50 for pyrosequencing. Its clinical application is to detect the presence or absence of known mutations within a specific segment of DNA of a single nucleotide polymorphism.

"Because mutations in melanoma appear to cluster in the BRAF, NRAS, and KIT genes, this molecular platform has been readily incorporated into the mutational analysis of melanoma," the authors explained, noting that pyrosequencing is a rapid and sensitive test for detection of more common BRAF V600E mutations, as well as other variants. It is limited to the length of the DNA template sequenced, and is prone to errors reading through homopolymer sequences.

• Allele-Specific Real-Time PCR. This molecular platform, also known as the amplification-refractory mutation system, enriches known mutations in clinical samples to increase sensitivity of detection, and is particularly useful in FFPE biopsies with low tumor content. It is highly sensitive and is confined to known BRAF mutations that occur in melanomas, but demonstrates greater sensitivity in detecting BRAF V600E mutations in FFPE clinical samples.

• Mass Spectrometry–Based Sequencing (Sequenom). Sequenom uses mass spectrometry to determine the sequence of the FFPE tissue samples of melanoma. The platform allows for simultaneous amplification of multiple genetic hot spots, allowing for analysis of several known mutations in a single clinical sample. In the authors’ experience, it has slightly higher sensitivity than pyrosequencing.

• High Resolution Melting (HRM). Also a highly sensitive method for screening for mutations in clinical samples, high-resolution melting relies on PCR amplification of the DNA template and analysis of the temperature gradient in which the double strands of the PCR products are melted. The strands melt at different temperatures, depending on the sequence of the constituent bases, allowing for detection of the mutant allele in the FFPE tissue sample. An important limitation of this approach is that specific nucleotide alteration is not reported, thus tissues samples that are positive for mutations will require additional sequencing by another method to determine the specific nucleotide alteration.

• The 454 Pyrosequencing (Roche). This powerful platform, one of several next generation sequencing technologies that allows ultra deep sequencing of entire exons, was used to resolve mutation discrepancies between the cobas 4800 BRAF V600 test and the Sanger sequencing method during the vemurafenib trials, the authors noted. It has a mean error rate of only 1.07%, with more than half of the errors at sites of homopolymers, has the lengths of individual reads of DNA sequences of more than 500 base pairs, and can be performed in less than a day.

• Cobas 4800 BRAF V600 Mutation Test. The cobas 4800 BRAF V600 Mutation Test is based on the principles of allele-specific real time PCR, and targets a predefined 116-base pair sequence of the BRAF gene on exon 15. The device, which is intended to identify those with BRAF V600E who might benefit from therapy with vemurafenib, has a sensitivity for detecting BRAF V600E on FFPE samples of melanoma of more than 99%, and a specificity of 88%. The sensitivity appears comparable with the other platforms, including Sequenom and HRM.

Although the platform is not designed to screen for nonrecurrent genetic mutations in melanoma, BRAF V600E appears to account for the highest percentage of mutations in cutaneous melanomas, the authors said.

Cutaneous Lymphoma Analysis

In cutaneous lymphomas, molecular analysis serves to confirm the diagnosis in cases in which the clinical and/or pathologic presentations do not provide a diagnosis and to further characterize the nature of the lymphoma, according to Dr. Janyana M.D. Deonizio and Dr. Joan Guitart.

While the gold standard for diagnosis is a solid clinicopathologic correlation, molecular analysis provides for a more concrete diagnosis that helps both the patient in facing the diagnosis, and the clinician in proceeding with the most appropriate treatment plan (Sem. Cut. Med. Surg. 2012;31:234-40).

Specifically, through immunophenotyping and clonality analysis, molecular analysis helps discern whether the lymphoma is primarily cutaneous or systemic with secondary skin involvement, and it subclassifies the tumor.

Methods for establishing T-cell clonality include Southern blot analysis (SBA) and PCR for detection of specific T-cell receptor gene arrangements (TCR-GR). SBA used to be the gold standard, but has been gradually replaced by PCR techniques which are less laborious and lengthy. PCR sensitivity for T-cell clonality detection ranges from 70% to 90%.

"Ideally, TCR clonality should be checked at the time of diagnosis in skin and blood. ... The detection of a dominant clone is important not only to confirm diagnosis but also for some prognostic guidance," they wrote, explaining that T-cell cloning is particularly helpful when early-stage mycosis fungoides is being considered in the differential diagnosis.

It does have limitations, however. False-positive monoclonal or oligoclonal bands may be identified in inflammatory dermatoses when T-cell infiltrates are sparse, resulting in "pseudomonoclonality," which is infrequently associated with a malignant T-cell process, they noted.

"Repeating the analysis using the same DNA template or fresh DNA extraction may solve the problem because in reactive conditions, the predominant PCR products typically vary in repeated PCR analyses of the same sample. In contrast, in neoplastic T-cell proliferations, dominant TCR clones are reproducible and should be routinely verified to confirm monoclonality," they noted.

Some studies suggest a correlation between TCR clonality by PCR and response to treatment; the absence of a detectable clone in cutaneous T-cell lymphoma (CTCL) has been associated with a higher rate of complete remission – although not necessarily with improved survival.

Immunophenotypic and immunogenotypic assays have been used to monitor the response of CTCL to therapy, define remission, and detect early relapse, thereby improving assessment of disease activity.

Flow cytometry analysis, for example, is "an efficient and sensitive method to detect and enumerate abnormal cells in the peripheral blood or any other cell suspension," they wrote. It can also be performed on leukocyte suspension from skin biopsies, and it provides prognostic information.

"Lower counts of circulating CD8+ lymphocytes and higher white cell counts in CTCL patients are associated with a less favorable prognosis," the authors noted.

FISH is used to detect major chromosomal gains or losses and specific translocations using a target-specific probe. Although FISH is not routinely used in the diagnosis of cutaneous lymphomas, it does appear to have potential future applications in various areas, according to recent publications.

Finally, genomic analysis by microarray-based comparative genomic hybridization is allowing quantification and appositional defining of chromosomal imbalances. While still confined to the research arena, this technology is providing some insight into the molecular pathogenesis of CTCL, the reported.

The advances in molecular diagnostics that are outlined in this series of articles are not limited to skin cancers and tumors. Additional articles, for example, addressed the role of genetic and molecular analysis in alopecia and in genodermatoses. Together they underscore the need for, and substantiate the ability of the specialty to take on leadership roles in molecular medicine, noted Dr. Gerami, of the department of dermatology at Northwestern University in Chicago.

"I am hopeful that they can assist other practicing dermatologists and dermatopathologists acquire a better foundation in molecular medicine, allowing them to sustain their primary roles in cutaneous medicine," Dr. Gerami concluded.

The authors reported having no conflicts of interest.