Havish S. Kantheti

The University of Texas Southwestern Medical Center

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Nikolaus Schultz

Memorial Sloan Kettering Cancer Center

Francisco Sánchez-Vega

Memorial Sloan Kettering Cancer Center

Walid K. Chatila

Memorial Sloan Kettering Cancer Center

Christopher A. Barker

Memorial Sloan Kettering Cancer Center

Charlotte E. Ariyan

Memorial Sloan Kettering Cancer Center

Jedd D. Wolchok

Cornell University

Matthew Meyerson

Harvard University

Paul B. Chapman

Memorial Sloan Kettering Cancer Center

Andrew D. Cherniack

Broad Institute

Ritika Kundra

Memorial Sloan Kettering Cancer Center

Cooperative Institutions

The University of Texas MD Anderson Cancer Center

130

National Institutes of Health

126

Memorial Sloan Kettering Cancer Center

107

Harvard University

Washington University in St. Louis

Baylor College of Medicine

Broad Institute

Dana-Farber Cancer Institute

National Cancer Institute

Canada's Michael Smith Genome Sciences Centre

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Table S4 from Therapeutic Implications of Detecting MAPK-Activating Alterations in Cutaneous and Unknown Primary Melanomas

Alexander N. Shoushtari Walid K. Chatila Arshi Arora Francisco Sanchez‐Vega Havish S. Kantheti

Univariate analysis of TTF outcomes to PD-1 monotherapy.

Table (database)

Primary (astronomy)

10.1158/1078-0432.22480397.v1

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Table S2 from Therapeutic Implications of Detecting MAPK-Activating Alterations in Cutaneous and Unknown Primary Melanomas

Alexander N. Shoushtari Walid K. Chatila Arshi Arora Francisco Sanchez‐Vega Havish S. Kantheti

Clinical data for each sequenced sample.

Table (database)

10.1158/1078-0432.22480403.v1

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Table S6 from Integrative Molecular Characterization of Malignant Pleural Mesothelioma

Julija Hmeljak Francisco Sánchez-Vega Katherine A. Hoadley Juliann Shih Chip Stewart

Table S6 contains results from the analysis of DNA methylation in SETD2 mutated and BAP1 inactivated samples.

BAP1

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10.1158/2159-8290.22534481

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Regulators of G protein Signaling (RGS) proteins (version 2020.5) in the IUPHAR/BPS Guide to Pharmacology Database

IUPHAR/BPS Guide to Pharmacology CITE (2020)

Katelin E. Ahlers‐Dannen Mohammed Alqinyah Christopher Bodle Josephine Bou Dagher Bandana Chakravarti

Regulator of G protein Signaling, or RGS, proteins serve an important regulatory role in signaling mediated by G protein-coupled receptors (GPCRs). They all share a common RGS domain that directly interacts with active, GTP-bound Gα subunits of heterotrimeric G proteins. RGS proteins stabilize the transition state for GTP hydrolysis on Gα and thus induce a conformational change in the Gα subunit that accelerates GTP hydrolysis, thereby effectively turning off signaling cascades mediated by GPCRs. This GTPase accelerating protein (GAP) activity is the canonical mechanism of action for RGS proteins, although many also possess additional functions and domains. RGS proteins are divided into four families, R4, R7, R12 and RZ based on sequence homology, domain structure as well as specificity towards Gα subunits. For reviews on RGS proteins and their potential as therapeutic targets, see e.g. [183, 411, 446, 450, 451, 558, 566, 345, 9].

RGS2

Gq alpha subunit

GTP-binding protein regulators

Gi alpha subunit

G beta-gamma complex

10.2218/gtopdb/f891/2020.5

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Table S7 from Integrative Molecular Characterization of Malignant Pleural Mesothelioma

Julija Hmeljak Francisco Sánchez-Vega Katherine A. Hoadley Juliann Shih Chip Stewart

Table S7 contains microbe screening results.

Table (database)

10.1158/2159-8290.22534478.v1

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Figure S1 from Therapeutic Implications of Detecting MAPK-Activating Alterations in Cutaneous and Unknown Primary Melanomas

Alexander N. Shoushtari Walid K. Chatila Arshi Arora Francisco Sanchez‐Vega Havish S. Kantheti

CONSORT diagram of samples that underwent MSK-IMPACT sequencing and analyzed for clinical outcomes with frontline PD-1 based therapy.

Primary (astronomy)

10.1158/1078-0432.22480418

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Table S4 from Therapeutic Implications of Detecting MAPK-Activating Alterations in Cutaneous and Unknown Primary Melanomas

Alexander N. Shoushtari Walid K. Chatila Arshi Arora Francisco Sanchez‐Vega Havish S. Kantheti

Univariate analysis of TTF outcomes to PD-1 monotherapy.

Univariate

Table (database)

Primary (astronomy)

Univariate analysis

10.1158/1078-0432.22480397

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Data from Therapeutic Implications of Detecting MAPK-Activating Alterations in Cutaneous and Unknown Primary Melanomas

Alexander N. Shoushtari Walid K. Chatila Arshi Arora Francisco Sanchez‐Vega Havish S. Kantheti

<div>AbstractPurpose:Cutaneous and unknown primary melanomas frequently harbor alterations that activate the MAPK pathway. Whether MAPK driver detection beyond BRAF V600 is clinically relevant in the checkpoint inhibitor era is unknown.Experimental Design:Patients with melanoma were prospectively offered tumor sequencing of 341–468 genes. Oncogenic alterations in 28 RTK-RAS-MAPK pathway genes were used to construct MAPK driver groups. Time to treatment failure (TTF) was determined for patients who received first-line programmed cell death protein 1 (PD-1) monotherapy, nivolumab plus ipilimumab, or subsequent genomically matched targeted therapies. A Cox proportional hazards model was constructed for TTF using driver group and clinical variables.Results:A total of 670 of 696 sequenced melanomas (96%) harbored an oncogenic RTK-RAS-MAPK pathway alteration; 33% had ≥1 driver. Nine driver groups varied by clinical presentation and mutational burden. TTF of PD-1 monotherapy (N = 181) varied by driver, with worse outcomes for NRAS Q61 and BRAF V600 versus NF1 or other alterations (median 4.2, 7.5, 22, and not reached; P < 0.0001). Driver group remained significant, independent of tumor mutational burden and clinical features. TTF did not vary by driver for nivolumab plus ipilimumab (N = 141). Among 172 patients with BRAF V600 wild-type melanoma who progressed on checkpoint blockade, 27 were treated with genomically matched therapy, and eight (30%) derived clinical benefit lasting ≥6 months.Conclusions:Targeted capture multigene sequencing can detect oncogenic RTK-RAS-MAPK pathway alterations in almost all cutaneous and unknown primary melanomas. TTF of PD-1 monotherapy varies by mechanism of ERK activation. Oncogenic kinase fusions can be successfully targeted in immune checkpoint inhibitor–refractory melanoma.</div>

10.1158/1078-0432.c.6530441.v1

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Table S1 from Integrative Molecular Characterization of Malignant Pleural Mesothelioma

Julija Hmeljak Francisco Sánchez-Vega Katherine A. Hoadley Juliann Shih Chip Stewart

Table S1 contains cohort description, Master Patient Table and MutSigCV results.

Table (database)

10.1158/2159-8290.22534508.v1

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Supplementary Data from Integrative Molecular Characterization of Malignant Pleural Mesothelioma

Julija Hmeljak Francisco Sánchez-Vega Katherine A. Hoadley Juliann Shih Chip Stewart

Supplementary materials and methods, as well as supplementary figures S1-S7.

Characterization

10.1158/2159-8290.22534517

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