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Posts Tagged ‘Resistance’


Immunotherapy Resistance Rears Its Ugly Head Again: PD-1 Resistant Metastatic Melanoma and More

Curator/Reporter: Stephen J. Williams, Ph.D.

From GenomeWeb

Source: https://www.genomeweb.com/sequencing/immune-gene-mutations-found-immunotherapy-resistant-metastatic-melanoma-patients?utm_source=SilverpopMailing&utm_medium=email&utm_campaign=Daily%20News:%20U%20of%20Texas%20Southwestern%20Medical%20Center%20Licenses%20Exosome%20Tech%20to%20Peregrine%20Pharmaceuticals%20-%2007/14/2016%2011:05:00%20AM

Immune Gene Mutations Found in Immunotherapy-Resistant Metastatic Melanoma Patients

NEW YORK (GenomeWeb) – Researchers from the US and the Netherlands reported in the New England Journal of Medicine that they have identified mutations in immune system-related genes in individuals who initially responded to anti-PD-1 treatment for metastatic melanoma treatment, but relapsed after six months or more.

A team led by investigators at the University of California at Los Angeles, the Jonsson Comprehensive Cancer Center, and the Netherlands Cancer Institute did exome sequencing on tumor samples from four individuals with metastatic melanoma prior to treatment with pembrolizumab (marketed as Keytruda by Merck). The researchers also assessed protein-coding sequences in tumor samples taken after late relapse, comparing the baseline and relapse tumors to search for mutations related to checkpoint blockade therapy resistance.

They uncovered suspicious mutations in three of the four individuals. In one individual, for example, they saw a truncating mutation affecting the beta-2-microglobulin (B2M) gene, which contributes to expression of class I major histocompatibility complex molecules recognized by the immune system’s CD8 T cells. Two more relapse tumors contained loss-of-function mutations to JAK1 or JAK2 — genes coding for interferon-related kinase enzymes.

“The mutations make the tumor resistant to the way the immune system tries to kill it,” first author Jesse Zaretsky, an MD/PhD student in senior author Antoni Ribas’ University of California at Los Angeles lab, told GenomeWeb. For example, he explained, the JAK mutations “are associated with the interferon receptor and make the tumors insensitive to the signals the immune system sends to slow [tumor] growth and kill the cancer.”

While roughly three-quarters of individuals treated with anti-PD-1 therapies show durable treatment responses, acquired resistance can occur, even long after immunotherapy-mediated tumor regression.

“With the approval of PD-1 checkpoint blockade agents for the treatment of patients with melanoma, lung cancer, and other cancers, it is anticipated that cases of late relapse after initial response will increase,” the study’s authors wrote. “Understanding the molecular mechanisms of acquired resistance … may open options for the rational design of salvage combination therapies or preventative interventions and may guide mechanistic biomarker studies for the selection of patients, before the initiation of treatment, who are unlikely to have a response.”

The team started with 78 metastatic melanoma patients who were treated with pembrolizumab at UCLA. Of the 42 individuals who showed an objective response to the checkpoint blockade therapy, 15 eventually experienced disease progression.

From that group of 15 patients, the researchers focused on four patients with late-acquired resistance — six months or more after response to pembrolizumab as a single agent — for whom there was sufficient biopsy material and clinical information available. Each of the patients had been receiving continuous doses of the drug until relapse, which occurred after a mean of nearly 21 months.

When the investigators scrutinized biopsies from the relapse tumors, they saw enhanced PD-L1 expression at the edges of tumors, along with CD8 T cells attempting to infiltrate the tumors. After capturing protein-coding portions of the genome in baseline and relapse tumor samples with Nimblegen exome kits, the team sequenced the exomes to nearly 150-fold average coverage using the Illumina HiSeq 2000.

“We wanted to capture all of the mutations down to low allele frequencies to get a picture of everything that was going on in the tumors, both before they went on the treatment and after [the tumors] came back,” Zaretsky said.

In the two cases marked by new JAK1 or JAK2 mutations at relapse, the team found that 93 percent to nearly 96 percent of baseline tumor mutations persisted in the relapse tumors.

The researchers suspect resistance mutations arose from clonal populations in the metastatic tumors that expanded after anti-PD-1 treatment. From allele frequency patterns in the relapsed tumors with JAK1/2 mutations, for example, they concluded that “tumors resistant to anti-PD-1 are a relatively homogeneous population derived directly from the baseline tumor and that acquisition of the JAK mutations was an early founder event.”

Even so, they didn’t detect burgeoning resistance mutations in the pre-pembrolizumab-treatment tumors, Zaretsky said, perhaps because such alterations were present in very few cells in the baseline tumors.

In cell lines established from the individual with JAK2 loss-of-function mutations at relapse, the team’s NanoString Technologies’ nCounter expression experiments pointed to loss of JAK2 protein expression after treatment progression, along with a dip in interferon gamma activity and diminished production of proteins involved in antigen presentation and T cell activity.

Other articles related to ImmunoOncology in this Open Access Journal include:

Vectorisation Of Immune Checkpoint Inhibitor Antibodies

First Drug in Checkpoint Inhibitor Class of Cancer Immunotherapies has demonstrated Superiority over Standard of care in the treatment of First-line Lung Cancer Patients: Merck’s Keytryda

Durable responses with checkpoint inhibitor

Immune-Oncology Molecules In Development & Articles on Topic in @pharmaceuticalintelligence.com

 

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Resistance to Receptor of Tyrosine Kinase

Curators: Larry H Bernstein, MD, FCAP and Aviva Lev-Ari, PhD, RN

Two just published articles in Science Translational Medicine report

(1) the discovery of bypass mechanisms of resistance to the receptor of tyrosine kinase inhibition (rTKI) in lung cancer
(2) receptor signaling networks in predicting drug response

Bypass Mechanisms of Resistance to Receptor Tyrosine Kinase Inhibition in Lung Cancer

Matthew J. Niederst1,2 and Jeffrey A. Engelman1,2*
1 Massachusetts General Hospital Cancer Center, Charlestown, MA
2 Department of Medicine, Harvard Medical School, Boston, MA
Sci. Signal., 24 Sep 2013; 6(294), p. re6
http://dx.doi.org/10.1126/scisignal.2004652

Abstract: Receptor tyrosine kinases (RTKs) are activated by somatic genetic alterations in a subset of cancers, and

  • such cancers are often sensitive to specific inhibitors of the activated kinase.

Two well-established examples of this paradigm include

  • lung cancers with either EGFR mutations or
  • ALK translocations.

In these cancers, inhibition of the corresponding RTK

  • leads to suppression of key downstream signaling pathways, such as
    • the PI3K (phosphatidylinositol 3-kinase)/AKT and
    • MEK (mitogen-activated protein kinase kinase)/ERK (extracellular signal–regulated kinase) pathways,

resulting in cell growth arrest and death.

Despite the initial clinical efficacy of ALK (anaplastic lymphoma kinase) and EGFR (epidermal growth factor receptor) inhibitors in these cancers,

  • resistance invariably develops, typically within 1 to 2 years.

Over the past several years, multiple molecular mechanisms of resistance have been identified, and some common themes have emerged. These are

  1. the development of resistance mutations in the drug target that prevent the drug from effectively inhibiting the respective RTK.
  2. activation of alternative RTKs that maintain the signaling of key downstream pathways
    • despite sustained inhibition of the original drug target.

Indeed, several different RTKs have been implicated in promoting resistance to EGFR and ALK inhibitors in both laboratory studies and patient samples.

In this mini-review, we summarize

  1. the concepts underlying RTK-mediated resistance,
  2. the specific examples known to date, and
  3. the challenges of applying this knowledge to develop improved therapeutic strategies to prevent or overcome resistance.

* Corresponding author. E-mail: jengelman@partners.org

Citation: M. J. Niederst, J. A. Engelman, Bypass Mechanisms of Resistance to Receptor Tyrosine Kinase Inhibition in Lung Cancer. Sci. Signal. 6, re6 (2013).

Profiles of Basal and Stimulated Receptor Signaling Networks Predict Drug Response in Breast Cancer Lines

Mario Niepel1*{dagger}, Marc Hafner1{dagger}, Emily A. Pace2{dagger}, Mirra Chung1, Diana H. Chai2, Lili Zhou1, Birgit Schoeberl2, and Peter K. Sorger1*
1 Harvard Medical School Library of Integrated Network-based Cellular Signatures Center, Department of Systems Biology, Harvard Medical School, Boston, MA
2 Merrimack Pharmaceuticals, Cambridge, MA
Sci. Signal., 24 Sep 2013; 6(294), p. ra84
Abstract: Identifying factors responsible for variation in drug response is essential for the effective use of targeted therapeutics. We profiled signaling pathway activity in a collection of breast cancer cell lines
  • before and after stimulation with physiologically relevant ligands, which
  • revealed the variability in network activity among cells of known genotype and molecular subtype.
Despite the receptor-based classification of breast cancer subtypes, we found that
  • the abundance and activity of signaling proteins in unstimulated cells (basal profile), as well as
  • the activity of proteins in stimulated cells (signaling profile),
varied within each subtype.
Using a partial least-squares regression approach, we constructed models that significantly predicted sensitivity to 23 targeted therapeutics. For example,
  • one model showed that the response to the growth factor receptor ligand heregulin effectively predicted
    • the sensitivity of cells to drugs targeting the cell survival pathway mediated by PI3K (phosphoinositide 3-kinase) and Akt, whereas
    • the abundance of Akt or the mutational status of the enzymes in the pathway did not.
Thus, basal and signaling protein profiles may yield new biomarkers of drug sensitivity and enable the identification of appropriate therapies in cancers characterized by similar functional dysregulation of signaling networks.
* Corresponding author. E-mail: peter_sorger@hms.harvard.edu (P.K.S.); mario_niepel@hms.harvard.edu (M.N.)
Citation: M. Niepel, M. Hafner, E. A. Pace, M. Chung, D. H. Chai, L. Zhou, B. Schoeberl, P. K. Sorger, Profiles of Basal and Stimulated Receptor Signaling Networks Predict Drug Response in Breast Cancer Lines. Sci. Signal. 6, ra84 (2013).

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