Jaime Rosenberg

Aiming to better select panels and models for accurate prediction of tumor mutational burden (TMB), researchers are proposing cancer-specific panels for an array of malignancies, which they say can help better select the appropriate patients for immune checkpoint inhibitor treatment.

The researchers analyzed the prevalence of mutations across the cancers, finding high variability.

“In view of the significant variability among different types of tumor, a cancer-specific strategy was used to design panels for TMB prediction,” wrote the researchers, “After excluding the largest genes, we selected for each cancer type the genes with mutations in ≥1% of the samples. Samples with mutations in at least one of these ‘gene-sets’ were used for further analysis.”

Based on their analysis, the researchers compiled a recommended number of genes to include in panels for each of the cancer types:

The proportion of genes that overlapped in the panels for the different cancer types ranged from 0% to 40%. In some cases, such as urinary tract or non-melanoma skin tumor, the percentage never reached 10%.

In order to test the association of the TMBs estimated in each of the recommended panels with outcomes to immune checkpoint inhibitor treatment, the researchers drew on data from a published cohort of 174 patients with metastatic melanoma and a cohort of 34 patients with NSCLC.

“First, we predicted the TMB for each sample using our suggested panels of 126 genes (0.79 Mb) for melanoma and 175 genes (0.97Mb) for NSCLC. As expected, predicted TMBs showed an excellent correlation with the published, experimental TMBs (R2=0.96 and 0.84 for melanoma and lung, respectively),” explained the researchers.

In their analysis, they found that a threshold of 150 mutations showed the best correlation with response to treatment. “Response rate of melanoma patients with >150 predicted mutations was 51%, compared with 18% in those with <150 predicted mutations.”

Median overall survival (OS) among patients with high predicted TMB was 24.3 months, more than double that of patients with low predicted TMB, who had an OS of 10.1 months.

The researchers found similar results when looking at the NSCLC cohort, with 56% of patients with high predicted TMB achieving a partial response to TCB treatment compared with 175 of patients with low TMB.

Martínez-PérezE, Molina-Vila M, Marino, Buslje C. Panels and models for accurate prediction of tumor mutation burden in tumor samples. 

. Published online April 13, 2021. doi:10.1038/s41698-021-00169-0

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Based on their analysis, the researchers compiled a recommended number of genes to include in panels for 14 cancer types.

Model Predicts Which Patients Will Respond to Immune Checkpoint Inhibitors

As ongoing studies continue to investigate which novel therapies can have a positive impact in myelodysplastic syndromes (MDS) and chronic myelomonocytic leukemia (CMML), researchers have published a rundown on which of these treatments have shown promise thus far.

Both MDS and CMML have variable symptom burdens and a risk of progression to acute myeloid leukemia.

“Allo-HCT remains the only curative therapy for both MDS and CMML but despite the more frequent use of reduced-intensity conditioning regimens and alternative grafts, as well as advances in supportive care, the majority of patients are not eligible for [allogeneic hematopoietic cell transplant] and are treated with [hypomethylating agents],” wrote the researchers.

With suboptimal response rates to standard of care hypomethylating agents (HMAs), there’s a need for more novel approaches that offer stronger and more durable responses, wrote the researchers. Recently, an oral version of decitabine, a drug typically used in this setting, gained FDA approval.

Concurrently, several targeted therapies are in development, although none have yet been approved. The researchers credit wider availability of molecular testing and better understanding of the diseases for the emerging targeted therapies in development.

“Molecularly driven agents such as IDH1/2 inhibitors, venetoclax, magrolimab, and APR-246 for MDS, as well as tagraxofusp, tipifarnib, and lenzilumab for CMML are being evaluated in various stages of clinical trials but more data are needed prior to their use in routine clinical practice,” wrote the researchers.

Preliminary results from the phase 2 portion of a phase 2/3 IMerge trial of telomerase inhibitor imetlelstat in patients with erythropoiesis-stimulating agent-refractory low-risk MDS showed a 42% 8-week red blood cell-transfusion independence (RBC-TI) rate and a 32% 24-week RBC-TI rate. Data from the phase 3 portion of the study are anticipated.

The oral hypoxia-inducible factor (HIF)-prolyl hydroxylase inhibitor roxadustat is being investigated for the treatment of anemia in patients with LR-MDS in a phase 2/3 trial of patients with transfusion-dependent LR-MDS who have serum RPO levels of <400 mIU/L. Early results from the study have showed a 38% 8-week RBC-TI and a 17% 20-week RBC-TI.

In both MDS and CMML, p53-refolding agent APR-246 has showed promise and is currently being evaluated in combination with AZA in a phase 3 trial of patients with 

“Due to the rarity of the disease, dedicated trials in CMML patients have been difficult to conduct,” note the researchers. “However, several novel agents are currently being studied in early phase trials in CMML patients.”

Potential novel treatments in this setting include:

Tipifarnib, a farnesyltransferase inhibitor that has been shown to be well-tolerated although with limited efficacy

Tagraxofusp, an anti-CD123 antibody, with preliminary results from a phase 1/2 study showing that the treatment elicited a spleen response in all 8 patients with baseline splenomegaly and mCRs in 2 pateints

Lenzilumab, an anti-GM-CSF antibody that has demonstrated safety and moderate efficacy in a phase 1 trial of 15 patients with CMML

Bewersdorf J, Zeidan A. Risk-adapted, individualized treatment strategies of myelodysplastic syndromes (MDS) and chronic myelomonocytic leukemia (CMML). 

The researchers credit wider availability of molecular testing and better understanding of the diseases for the emerging targeted therapies in development.  

MDS, CMML Pipelines Inch Closer to Arrival of Targeted Therapies

 the most recent developments in prognostic markers and treatment advances in 

 (PV), including pegylated interferon-alpha 2 (IFN-alfa-2a), mouse double-minute homolog 2 (MDM2) antagonists, hepcidin mimetics, and histone deacetylase inhibitors.

The review comes amid growing attention directed at identifying treatments that can prevent progression of PV to myelofibrosis or an aggressive form of acute myeloid leukemia.

“Ultimately, the goals of therapy in this chronic disease are to improve quality of life, reduce risk of thrombosis, and alter disease course,” wrote the pair. “The therapeutic landscape of PV is evolving because of a more thorough understanding of the molecular mechanisms driving the pathogenesis and progression of this disease.”

For example, some focus has been paid to combining pegylated interferon (IFN) with agents like ruxolitinib. A phase 2 study looking at the treatment combination in 32 patients with PV and myelofibrosis showed a 31% remission rate and 9% complete remission rate. Notably, the study also showed that a significant number of patients cannot tolerate IFN-alfa-2a, with nearly one-third of patients in the study dropping out, likely due to the side effects of the treatment.

Another phase 2 randomized study is currently assessing the effects of ropeginterferon-alfa-2b compared with phlebotomy alone in patients with low-risk PV. Interim results indicated that 84% of patients receiving the IFN-alfa-2a treatment met the primary endpoint of percentage of patients maintaining a hematocrit of not more than 45% over 1 year without evidence of disease progression (

 = .008). In comparison, 60% of patients receiving phlebotomy alone met the endpoint.

MDM2 inhibitors have also been suggested as an attractive treatment class. A phase 1 study of patients with refractory PV receiving oral MDM2 antagonist idasanutlin showed a 58% response rate and a 50% response rate when the treatment was combined with IFN-alfa-2a treatment.

Results from a phase 2 study of the nutlin KRT-232 are anticipated. The study includes phlebotomy-dependent patients with PV.

With iron deficiency being a prevalent issue among patients with PV, the addition of hepcidin agonists is being explored to restrict systemic iron metabolism. PTG-300 is currently being studied in a phase 2 trial of 13 patients with PV, with preliminary findings indicating that the treatment is both safe and tolerable. All patients have maintained hematocrit of less than 45% without phlebotomy for up to 7 months, and iron deficiency appears to be reversing based on increasing ferritin, iron, and transferrin saturation levels.

A fourth class of treatment, histone deacetylase inhibitors, is also being explored. Givinostat was tested in a phase 1b/2 study of patients with PV, which established the maximum tolerated dose of the treatment to be 100 mg twice a day. Study results also showed a high response rate.

“Further study is needed to determine whether these agents have a role in reducing thrombosis risk and preventing disease progression to myelofibrosis and myeloproliferative neoplasms blast phase,” researchers said.

“Given that PV is a chronic disease, it is essential that these therapeutics be safe and tolerable to allow for prolonged treatment. The future of PV treatment likely will require combination treatments, which are being explored in preclinical studies," they concluded.

Marcellino BK and Hoffman R. Recent advances in prognostication and treatment of polycythemia vera. 

. Published online March 12, 2021. doi: 10.12703/r/10-29

The review comes amid growing attention directed at identifying treatments that can prevent progression of polycythemia vera (PV) to myelofibrosis or an aggressive form of acute myeloid leukemia. 

Several Treatment Classes Show Promise in Treatment of PV

Combining carfilzomib, a broad-spectrum drug with low toxicity, with bortezomib, a highly effective drug with cytotoxic side effects, may be a viable treatment strategy for 

, an aggressive cancer with poor survival, according to 

. If confirmed in future trials, the combination could provide these patients with an option that reduces the side effects of bortezomib.

The in vitro study of melanoma cells analyzed the molecular mechanisms of the pair of proteasome inhibitors, finding that they reduced B16-F1 tumor growth. The treatment combination also showed promise in a C67BL/6 xenograft mouse model, with researchers observing significant reductions in tumor size in the mice.

In the in vitro model, the combination inhibited tumor growth through apoptosis via endoplasmic reticulum (ER) stress and reactive oxygen species (ROS) accumulation, and mitochondrial membrane potential (MMP) loss in the melanoma cells.

“BZ- and CFZ-induced apoptosis were confirmed by the presence of cleaved caspase 3, 8, 9, and 12. Western blotting revealed that the overall effect of BZ on caspase activation was stronger than that of CFZ at the same concentration,” researchers wrote.

“In addition, the high level (10% compared to 2%) of fetal bovine serum (FBS) in the Dulbecco’s modified Eagle’s media (DMEM) reduced the caspase activation signals in BZ- and CFZ-treated cells. Time-dependent Western blot analyses with cells cultured in 2% FBS also showed that the activation of caspase 3 was evident at 24 h after treatment with 100 nM BZ and CFZ,” they said.

While bortezomib began to activate caspase 8, 9, and 12 after 16 hours and enhanced their activation at 24 hours, carfilzomib slightly activated caspase 9 and 12 at 16 hours but caspase 8 at 24 hours.

These findings, say the researchers, indicate that both treatments can induce apoptosis by activating canonical caspases that are implicated in the intrinsic and extrinsic pathways. However, they note that each treatment had different contributions.

“To determine ER stress induction, B16-F1 cells were treated with various concentrations of BZ and CFZ for 24 hours, and the expression of ER stress-associated proteins, such as GRP94, GRP78, soluble XBP1, and CHOP, and the cleavage of ATF6α was examined by Western blot analysis,” authors explained.

They continued, “the concentration-dependent Western blotting data clearly showed that the levels of some of the ER stress markers, such as GRP78, ATF6α, and XBP1, were greater in the BZ-treated cells than in the CFZ-treated cells at the same concentration.”

The researchers also tested the ability of the pair to induce ROS accumulation, finding that ROS levels increased from 11.7% to 45% with 100 nM of bortezomib treatment and to 37% with 100 nM of carfilzomib.

Lee MS, Lim SH, Yu A, Hwang CY, Kang I, and Yeo E. Carfilzomib in combination with bortezomib enhances apoptotic cell death in B16-F1 melanoma cells. 

. 2021;10(2):153. doi:10.3390/biology10020153

The in vitro study of melanoma cells analyzed the molecular mechanisms of the pair of proteasome inhibitors, finding that they reduced B16-F1 tumor growth.

Jaime Rosenberg

Articles

Model Predicts Which Patients Will Respond to Immune Checkpoint Inhibitors

MDS, CMML Pipelines Inch Closer to Arrival of Targeted Therapies

Several Treatment Classes Show Promise in Treatment of PV

Carfilzomib, Bortezomib Combo Shows Potential for Reducing Tumor Growth in Melanoma Cells