Recommendations for Specimen and Therapy Selection in Colorectal Cancer.

INTRODUCTION: Next-generation sequencing has emerged as a clinical tool for the identification of actionable mutations to triage advanced colorectal cancer patients for targeted therapies. The literature is conflicted as to whether primaries or their metastases should be selected for sequencing. Some authors suggest that either site may be sequenced, whereas others recommend sequencing the primary, the metastasis, or even both tumors. Here, we address this issue head on with a meta-analysis and provide for the first time a set of sensible recommendations to make this determination. METHODS: From our own series, we include 43 tumors from 13 patients including 14 primaries, 10 regional lymph node metastases, 17 distant metastases, and two anastomotic recurrences sequenced using the 50 gene Ion AmpliSeq cancer NGS panel v2. RESULTS: Based on our new cohort and a meta-analysis, we found that ~ 77% of patient-matched primary-metastatic pairs have identical alterations in these 50 cancer-associated genes. CONCLUSIONS: Low tumor cellularity, tumor heterogeneity, clonal evolution, treatment status, sample quality, and/or size of the sequencing panel accounted for a proportion of the differential detection of mutations at primary and metastatic sites. The therapeutic implications of the most frequently discordant alterations (TP53, APC, PIK3CA, and SMAD4) are discussed. Our meta-analysis indicates that a subset of patients who fail initial therapy may benefit from sequencing of additional sites to identify new actionable genomic abnormalities not present in the initial analysis. Evidence-based recommendations are proposed.

Comparison of Large, Medium, and Small Solid Tumor Gene Panels for Detection of Clinically Actionable Mutations in Cancer.

BACKGROUND: Next-generation sequencing of gene panels has supplanted single-gene testing for cancer molecular diagnostics in many laboratories. Considerations for the optimal number of genes to assess in a panel depend on the purpose of the testing. OBJECTIVE: To address the optimal size for the identification of clinically actionable variants in different-sized solid tumor sequencing panels. PATIENTS AND METHODS: Sequencing results from 480 patients with a large, 315 gene, panel were compared against coverage of a medium, 161 gene, and small, 50 gene, panel. RESULTS: The large panel detected a total of 2072 sequence variants in 480 patient specimens; 61 (12.7%) contained variants for which there is therapy approved by the US Food and Drug Administration, 89 (18.5%) had variants associated with an off-label therapy, and 312 (65.0%) contained variants eligible for a genomically matched clinical trial. The small panel covered only 737 of the 2072 variants (35.5%) and somewhat fewer therapy-related variants (on-label 88.5%, off-label 60.7%). The medium-size panel included 1354 of the 2072 (65.3%) variants reported by the large panel. All 318 patients with a clinically actionable variant would have been identified by the medium panel. CONCLUSIONS: The results demonstrate that a carefully designed medium size gene panel is as effective as a large panel for the detection of clinically actionable variants and can be run by most molecular pathology laboratories.

Next-Generation Sequencing: A Novel Approach to Distinguish Multifocal Primary Lung Adenocarcinomas from Intrapulmonary Metastases.

Distinguishing between multiple lung primary tumors and intrapulmonary metastases is imperative for accurate staging. The American Joint Committee on Cancer (AJCC) criteria are routinely used for this purpose but can yield equivocal conclusions. This study evaluated whether next-generation sequencing (NGS) using the 50-gene AmpliSeq Cancer Hotspot Panel version 2 can help facilitate this distinction. NGS was performed on known primary-metastatic pairs (8 patients) and multiple lung adenocarcinomas (11 patients). Primary-metastatic pairs had high mutational concordance. Seven pairs shared mutations, and 1 was concordant for having no mutations. Driver mutations in KRAS (n = 4), EGFR (n = 2), and BRAF (n = 1) were always concordant. Multiple lung tumors from 3 patients were completely concordant and predicted by NGS to be intrapulmonary metastases, whereas 8 had completely discordant mutations and were predicted to be independent primary tumors. The NGS prediction correlated with the AJCC (eighth edition) prediction in all patients for whom the latter was unequivocal (8 of 11). Furthermore, it separated patients by overall survival. Patients with predicted multiple independent primary tumors by NGS had better survival than those with distant metastases (P = 0.016, log-rank test), whereas those with predicted intrapulmonary metastases had no difference (P = 0.527). With further validation, the 50-gene panel has the potential to serve as an adjunct to the AJCC criteria.

Concurrent inhibition of MYC and BCL2 is a potentially effective treatment strategy for double hit and triple hit B-cell lymphomas.

Double hit lymphoma or triple hit lymphoma (DHL/THL) is a rare form of aggressive B-Cell Lymphoma. Overexpression of MYC, BCL2 or/and BCL6 due to genomic rearrangements are the key molecular features of DHL/THL. Patients with DHL/THL show very aggressive disease course and poor survival due to the lack of effective treatment modalities. Here, we established new THL cell model and assessed its in vitro growth characteristics along with the DHL cell line in response to potent MYC inhibitors, 10058-F4 and JQ-1, and a BCL2 inhibitor, ABT-199, with or without chemotherapeutic agent vincristine or doxorubicin. We found that 10058-F4, JQ-1 or ABT-199 exposure as a single agent inhibited the growth of DHL/THL cells in a dose-dependent manner. Combined exposure of 10058-F4 or JQ-1 and ABT-199 as well as vincristine or doxorubicin markedly suppressed the growth of DHL/THL cells compared with the single treatment. As assessed by multiple approaches, apoptosis induced by ABT-199, 10058-F4 or JQ-1 was underlying cause of the observed growth suppression. These findings suggest that co-inhibition of MYC and BCL2 signaling is a promising therapeutic strategy for patients with DHL/THL lymphomas.

BRAF genetic heterogeneity in papillary thyroid carcinoma and its metastasis.

Intratumoral heterogeneity is widely recognized as an important determinant of a cancer's initial response and its subsequent resistance to targeted therapy. BRAF V600E mutation, common in papillary thyroid carcinoma (PTC), is helpful in fine needle aspiration diagnosis of thyroid nodules and is being evaluated for targeted therapies. This study was designed to assess the presence of BRAF mutation heterogeneity within primary PTCs and between paired primary and metastatic lesions. Genetic heterogeneity was evaluated in 47 PTCs (38 differentiated papillary thyroid carcinomas and 9 poorly differentiated PTCs with anaplastic areas). The differentiated papillary thyroid carcinomas included 16 cases with regional lymph node metastases at thyroidectomy and 9 cases with recurrent metastases to regional lymph nodes more than 5 years post thyroidectomy. Genetic heterogeneity of BRAF was studied by comparing the mutation status in different samples of tumor as follows: (a) 2 separate areas (each >1.5 cm in diameter) within the primary tumor, (b) a more than 1.5 cm area of primary carcinoma and a second 5 mm area simulating a fine needle aspiration sample from a different portion of the primary tumor, (c) primary carcinoma and its lymph node metastasis at thyroidectomy, (d) primary carcinoma and the recurrent metastasis, and (e) differentiated and anaplastic areas in the primary carcinoma. BRAF mutation status was concordant in 95.2% of the 62 paired samples. Discordant BRAF status was detected in only 4.8% of the pairs studied and most frequently involved cases with recurrent metastasis thus suggesting a need for additional testing of these lesions before instituting therapy.

Significant reduction of ATP production in PHA-activated CD4+ cells in 1-day-old blood from transplant patients.

BACKGROUND: Global immunosuppression can be measured by assessing adenosine triphospate (ATP) levels in mitogen-stimulated CD4+ T cells. METHODS: We investigated the effect of storage time on ATP levels in 234 blood samples from 18 healthy individuals and 152 transplant patients. The difference between day 0 (<13 hours post-blood draw) and day 1 (24-37 hours) measurements was analyzed and compared with various factors; a subset of samples was also analyzed in 6-hour intervals. RESULTS: The ATP levels were significantly lower on day 1 compared with that on day 0 in healthy individuals (279±159 vs 414±159 ng/mL, P<0.001) and patients (356±209 vs 455±221 ng/mL, P<0.0001). Of the 18 healthy individuals, 17 showed ATP reduction, whereas 192 (89%) of 216 patients did so on day 1 (24.8±24.1%). In the time course analysis, ATP levels decreased with the blood storage time in healthy and patient samples, and the reduction began as early as 7 hours post-blood draw. The reduction rate was significantly higher in patient samples with low day 0 ATP levels compared with samples with moderate or high levels (44.7±31.3% vs 23.2±23.6% or 18.7±15.7%; P<0.001). The reduction rate in patients treated with alemtuzumab induction was slightly higher than that in daclizumab-treated patients (28.8±24.6% vs 21.3±21.3%, P=0.09). CD4+ cell number did not change within 24 hours post-blood draw, but CD4 expression decreased 2.0±2.8% (P<0.05). CONCLUSIONS: The ATP levels are significantly lower in 1-day-old blood compared with fresh blood, suggesting that fresh blood should be used for assessing the T cell immune function to obtain the most accurate results.

Immunologic parameters and viral infections in patients desensitized with intravenous immunoglobulin and rituximab.

Desensitization with IVIG and rituximab followed by transplantation with alemtuzumab or daclizumab induction is an effective clinical protocol. Here, we examined the effects of this protocol on immune cell number, T cell function by Cylex ImmuKnow®, CMV-specific CD8+ T cell (CMV-Tc) activity, total and viral-specific immunoglobulin levels and viral infections. In 17 highly HLA-sensitized (HS) patients who received desensitization, CD19+ cells were undetectable immediately after desensitization, while other immune cells were unchanged. No alteration in Cylex or CMV-Tc levels was seen. In separate 14 HS patients who were desensitized followed by transplantation, T cell numbers were near zero after alemtuzumab, while NK cell reduction was minimal. Early B cell recovery was not a risk for antibody-mediated rejection. Total IgG, IgM, and IgA remained in the normal range up to 12.6 months post-transplant, and CMV IgG level did not change. CMV-Tc activity was eliminated post-transplant in some patients, but recovered by 4 months post-transplant. None of them developed CMV infection. In conclusion, IVIG-rituximab-desensitization does not significantly alter T cell function pre-transplant, or reduce Ig levels below the normal range post-transplant. Although post-transplant induction therapy is associated with a transient depletion of viral-specific CD8+ memory cells, it does not increase risks for viral infections.

In vitro effects of everolimus and intravenous immunoglobulin on cell proliferation and apoptosis induction in the mixed lymphocyte reaction.

Targeting multiple pathways in the activation of alloimmune responses by multi-drug immunosuppressive regimens with complementary mechanisms of action enhances allograft survival and improves quality of life, owing to the reduction of adverse drug effects. In this report we investigated the effect of the combination of everolimus and intraveneous immunoglobulin (IVIG) on cell proliferation and apoptosis induction in human two-way mixed lymphocyte reaction (MLR). Everolimus alone (0.1-50 ng/ml) and IVIG (1-10 mg/ml) alone inhibited cell proliferation in a dose-dependent manner (16.4-67.2% and 12.1-66.3% inhibition, respectively). The inhibition by everolimus was not enhanced in the presence of 1 mg/ml IVIG. Addition of 10 and 50 ng/ml everolimus increased the inhibitory effect of 5 and 10 mg/ml IVIG, but only by 10-27%. Addition of 0.1 and 1 ng/ml everolimus did not increase IVIG's inhibitory effects. Apoptosis was significantly higher in IVIG (5 mg/ml)-treated CD19+ cells and less so in CD3+ cells as assessed by Annexin V and TUNEL assays. However, everolimus (0.1-50 ng/ml) did not induced apoptosis or alter apoptosis induced by IVIG. These results suggest that everolimus is a potent inhibitor of immune cell proliferation but does not act additively or synergistically with IVIG when analyzed in this in vitro system.

Cellular allo reactivity against paternal HLA antigens in normal multiparous females as detected by intracellular cytokine flow cytometry remains elevated over years despite diminution of anti-HLA antibody levels.

BACKGROUND: Sensitization to allo-antigens (Ags) resulting from previous transplants, blood transfusion or pregnancy (PG), is a significant obstacle to kidney transplantation and risk factor for antibody-mediated rejection (AMR). We have previously shown that allo-Ag-specific CD3 negative (-) cells as analyzed by cytokine flow cytometry (CFC) are elevated in many highly HLA-sensitized (HS) patients, but not most normal individuals. HS patients with high(+) CFC, especially to donor Ags, may be at high risk for AMR and may need additional pre-transplant desensitization. Here, we investigate allo-sensitization that results from paternal HLA (pHLA) Ag exposure in normal multiparous females and assess the utility of the CFC assay in detecting allo-Ag-specific immune cell activity. METHODS: Whole blood from 8 normal females with previous PG (pPG), 8 normal females without pPG and 5 normal males were incubated with irradiated normal peripheral blood mononuclear cells (PBMC). IFNgamma+/CD3- cells were enumerated and results expressed as a ratio against un-stimulated cells. RESULTS: 4/8 females with pPG showed elevated CFC reactivity against at least 1 PBMC tested (ratio 4.7+/-1.4), while the remaining 4 (0.76+/-0.42), 8 females without pPG (0.65+/-0.24) and 5 males (0.99+/-0.59) showed minimal reactivity. The reactivity against the same PBMC was fairly consistent over months and years. Anti-HLA antibody was detected in females with elevated CFC, but the levels as analyzed by ELISA did not correlate with CFC reactivity. Individuals with minimal reactivity consistently show negative anti-HLA antibody levels. Two females with pPG with elevated CFC (#1 and #2) showed high reactivity to PBMC from their husbands, one offspring and 3rd-party normals carrying antigenic pHLA-Ags (#1: 13.2, 9.4 and 22.9; #2: 8.2, 8.0 and 8.8-12.6, respectively). Antibody specificity for antigenic pHLA-Ags was found by Luminex in anti-HLA antibody(+) samples in these 2 females. CONCLUSIONS: 1) The CFC is a novel way to measure allo-specific CD3- cell responses and can detect allo-sensitization resulting from PG, 2) the CFC detects allo-specific memory cell activity as reactivity is consistent over years regardless of anti-HLA antibody levels, 3) high(+) CFC in normal multiparous females may explain increased risk for AMR in female HS patients, and 4) analysis of donor- or allo-specific CFC in multiparous females awaiting kidney transplant may identify those at risk for AMR.

Mycophenolic acid and intravenous immunoglobulin exert an additive effect on cell proliferation and apoptosis in the mixed lymphocyte reaction.

BACKGROUND: Intravenous immunoglobulin (IVIG) has known immunomodulatory effects in autoimmune diseases and transplantation and is commonly used in desensitization protocols and for treatment of antibody-mediated rejection (AMR). IVIG inhibits the MLR and induces apoptosis in immune cells. Mycophenolate mofetil inhibits immune cell proliferation and is an effective immunsuppressive agent. Here, we examined the possible synergistic effects of combined MMF and IVIG on cell proliferation and apoptosis induction in the MLR. METHODS: Two-way MLRs were performed with mycophenolic acid (MPA), IVIG and both in combination. Cell proliferation and apoptosis were detected by 3H-thymidine incorporation and Annexin flow cytometry, respectively. RESULTS: IVIG (1-10mg/ml) or MPA (0.01-0.25 microg/ml) alone inhibited cell proliferation in the MLR in a dose-dependent manner. MPA at 0.01-0.03 microg/ml showed minimal inhibition, but the addition of 5 and 10mg/ml IVIG increased inhibition significantly (p<0.05) to 43% and 64%, respectively. Annexin V positive cell number was significantly higher in IVIG (5mg/ml) treated CD19+ cells (68+/-13% vs. 43+/-12%, p=0.001) compared to untreated cells and to a lesser degree in CD3+ cells (29+/-7% vs. 25+/-10 %, p=0.02). MPA (0.25-10 microg/ml) alone neither induced nor inhibited apoptosis. Addition of MPA had no effect on apoptosis induced by IVIG. CONCLUSION: 1) Combining low concentrations of IVIG (5-10 mg/ml) and MPA (0.01-0.03 microg/ml)has an additive effect on inhibition of cell proliferation in the MLR. 2) MPA alone neither induces nor inhibits apoptosis in T or B cells in the MLR, and has no effect on apoptosis induced by IVIG. These in vitro observations may have implications for modification of therapeutic approaches to protocols utilizing IVIG for desensitization and immune modulation.

Intracellular IFNgamma production in CD3 negative cells exposed to allo-antigens is an indicator of prior sensitization.

BACKGROUND: Sensitization to HLA antigens (Ags) is a significant obstacle to kidney transplantation and risk factor for antibody-mediated rejection (AMR). Current screening methods to assess HLA Ag exposure include various antibody assays. However, tools to accurately measure cell-mediated immunity to allo-Ags in a clinical setting are lacking. Here we report on an intracellular cytokine flow cytometry (CFC) assay that detects intracellular gamma-interferon (IFNgamma) production in non-T cell populations (CD3-) that appears to assess sensitization from previous allo-Ag exposure. METHODS: Blood from 106 highly-HLA sensitized (HS) patients (pre-, post-IVIG-treatment [Rx] and/or post-transplant) and 14 3(rd) party normal controls (3(rd)N) were incubated with donor or 3(rd)N peripheral blood mononuclear cells (PBMCs), and IFNgamma+/CD3- cells were enumerated. RESULTS: The percentage of IFNgamma+ cells in CD3- cells without stimulation in pre-IVIG-Rx HS patients was similar to normals, but significantly increased with incubation with donor and/or 3(rd)N PBMCs. Reactivity in normals was minimal. Reactivity was higher in HS females than HS males. Normal females with previous pregnancy (PG) showed significantly higher response than females without PG or non-sensitized normal males. Donor-specific reactivity in the CFC assay better correlated with donor-specific B cell crossmatch than total anti-HLA antibody levels or PRA. HS patients who developed AMR post-transplant showed significantly higher reactivity than those without AMR. CONCLUSIONS: The CFC assay measures IFNgamma production in CD3- cells that may indicate a memory response to allo-Ags. This response is limited to HS patients and normal females with previous PG. Patients undergoing AMR show significantly higher reactivity. This assay may represent a novel approach to measurement of allo-sensitization with clinical utility in predicting those at risk for AMR.

Co-infection of polyomavirus-BK and cytomegalovirus in renal transplant recipients.

BACKGROUND: Polyomavirus-BK (BK) is a significant cause of allograft dysfunction in renal transplant recipients. Cytomegalovirus (CMV) and BK infection are thought to be possible risk factors for one another, but no supporting data are yet available. METHODS: The authors monitored BK and CMV infection by quantitative polymerase chain reaction (PCR) in 69 renal transplant recipients with serum creatinine elevation to determine the prevalence of co-infection. In addition, 150 adult renal transplant recipients were also retrospectively analyzed for both infections. RESULTS: Of 69 recipients, 12 were plasma BK-PCR-positive. Eight of the 12 showed high BK levels (>10 copies) and BK nephropathy. Six of the 12 were also CMV-PCR-positive compared with only 3 of 57 plasma BK-negative patients (50% vs. 5.3%, P=0.001). Comparatively, the incidence of Epstein-Barr virus infection was similar in both groups (1 of 12 [8.3%] vs. 2 of 57 [3.5%], P =not significant). In addition, retrospective analysis of CMV-PCR-positivity in 150 adult renal transplant recipients showed similar results (5 of 6 in BK-PCR-positive [83%] vs. 8 of 144 in BK-PCR-negative [5.6%], P=0.00001). More plasma BK-PCR-positive patients had concomitant CMV infection than CMV-PCR-positive patients with BK infection (5 of 6 [83%] vs. 4 of 13 [31%], P=0.05). CONCLUSIONS: In conclusion, high plasma BK-positivity (>10) is significantly associated with BK nephropathy. Plasma BK-positivity is highly associated with co-infection of CMV, suggesting possible risk factors for one another. Therefore, detection of either infection strongly suggests the need to monitor for the other. This strategy may lead to the prevention of virus-induced complications by preemptive antiviral therapy in renal allografts.

Immunomodulatory effects of combination of pooled human gammaglobulin and rapamycin on cell proliferation and apoptosis in the mixed lymphocyte reaction.

BACKGROUND: Multidrug immunosuppressive regimens benefit transplant recipients, reducing side effects and creating synergy between medications with different mechanisms of action. We have shown that pooled human gammaglobulin (intravenous immunoglobulin [IVIG]) inhibits the mixed lymphocyte reaction (MLR) and induces apoptosis primarily in B cells. Rapamycin (RAPA), a potent macrolide immunosuppressant, inhibits B- and T-cell proliferation through G1 cell-cycle blockade and purportedly induces apoptosis. Here we examined the possible synergistic effects of IVIG and RAPA on cell proliferation and apoptosis induction in the MLR. METHODS: MLR was performed with IVIG (0.2-5 mg/mL), RAPA (0.02-40 ng/mL), alone or in combination. Cell proliferation was detected by H-thymidine incorporation, and apoptosis by Annexin V and terminal deoxynucleotide transferase-mediated dUTP nick-end labeling flow cytometry. RESULTS: IVIG or RAPA inhibited cell proliferation in a dose-dependent manner. RAPA (0.02-40 ng/mL) in combination with IVIG (5 mg/mL) significantly augmented the inhibition compared with RAPA alone (70% vs. 34% at 0.2 ng/mL; 90% vs. 76% at 2 ng/mL). Apoptosis was significantly higher in IVIG-treated (5 mg/mL) CD19+ cells and less so in CD3+ cells. However, RAPA (0.2-40 ng/mL) neither induced apoptosis nor altered apoptosis induced by IVIG. CONCLUSIONS: Combined RAPA and IVIG at subtherapeutic concentrations inhibits cell proliferation in the MLR. RAPA neither induces apoptosis nor augments apoptosis induced by IVIG in the MLR. Lower-concentration RAPA (0.2-2 ng/mL) in combination with IVIG (5 mg/mL) versus therapeutic levels (2-50 ng/mL and 10-40 mg/mL, respectively) could represent an effective immunomodulatory drug combination.

Pooled human gammaglobulin modulates surface molecule expression and induces apoptosis in human B cells.

We have previously shown that the pooled human gammaglobulin (IVIG) inhibited mixed lymphocyte reaction (MLR). In this study, we examined (1) if IVIG contains blocking antibodies reactive with cell surface molecules required for alloantigen recognition and (2) if IVIG modulates these surface molecule expressions using flow cytometry. IVIG does not contain significant amounts of blocking antibodies against CD3, CD4, CD8, CD20, CD14, CD40, MHC class I and class II. It reduces the number of intact B cells and monocytes, reduces or modulates CD19, CD20 and CD40 expression on B cells, and induces morphological changes in B cells. This B-cell modulation results primarily because of apoptosis. IVIG also induces apoptosis in T cells and monocytes, but to a lesser degree. Induction of apoptosis requires the intact IgG molecule. Reduction of intact B cell and monocyte cell numbers, modulation of surface molecule expression on B cells, and deletion of B and T cells by apoptosis could result in inhibition of optimal T-cell activation. This likely represents the primary mechanism responsible for IVIG suppression of the MLR, and may account for many of the observed beneficial effects of IVIG seen in the treatment of human autoimmune and alloimmune disorders.