Mucinous tubular and spindle-cell carcinoma of the kidney: Clinical features, genomic profiles, and treatment outcomes.

Abstract

Background:

Mucinous tubular and spindle-cell carcinoma (MTSCC) is a rare kidney cancer subtype with limited cases reported in the literature. We report on outcomes of 25 patients with this variant who were managed at our institution.

Materials and Methods:

The institution database was queried, and clinical data extracted for patients with MTSCC. Molecular features examined included next generation sequencing with MSK-IMPACT and allele-specific copy number analysis using FACETS algorithm in a subset of patients.

Results:

All patients underwent primary tumor-directed therapy including (Nephrectomy=23, cryoablation=2). Metastases were diagnosed in 6 patients (24%), 3 of which had de novo metastatic disease. Five of 6 patients with metastatic disease had high grade histological features compared to 0 of 19 non-metastatic patients (83% vs 0%, p < 0.001, Fisher’s exact test). 3-year overall survival from diagnosis was 84.8% (95% CI: 59.6, 94.9) with a median follow-up time of 3.9 years (range:1 months, 10.3 years). Three deaths occurred, all from metastatic disease. Four patients received systemic therapy with time to treatment failure ≤ 6 months across different agents with the exception of one patient with prolonged response on sunitinib (30.6 months). Most frequent molecular alterations were NF2 mutations (n=2, 40%), germline alterations (n=2, 40%) including CHEK2 and BRCA2 mutations, multiple chromosomal copy number losses and mismatch repair deficiency in one patient.

Conclusions:

MTSCC is characterized by localized tumors treated successfully with primary tumor directed therapy. However, patients with high grade histological features were more likely to develop metastatic disease with limited responses to standard therapies.

MICRO ABSTRACT:

We studied cancer specifics outcomes of 25 patients with mucinous tubular and spindle-cell carcinoma of the kidney and we found that the majority of patients presented with localized tumor that were treated successfully with primary tumor directed therapy. However, those with high grade histological features were more likely to develop metastatic disease with limited responses to standard therapies.

Introduction

Renal cell carcinoma (RCC) encompasses a group of heterogeneous malignancies each with unique pathological, molecular and clinical features. The taxonomy of RCC has expanded over the last 3 decades and the most recent 2016 WHO classification included 12 recognized subtypes with several emerging entities¹. Mucinous tubular and spindle cell carcinoma (MTSCC) of the kidney is a rare subtype which was first described under a variety of terms including RCC with unusual differentiation², low-grade collecting duct carcinoma³, unusual RCC with prominent spindle cell change possibly related to the loop of Henle⁴, and subsequently recognized as a distinct RCC entity in the WHO 2004 classification of renal tumors⁵. It has a wide of age distribution with female predominance in most of the reported case series^6,7, and generally appreciated as a tumor of low malignant potential and low risk of metastasis^6-8. Few metastatic cases have been reported mainly in association with high grade and sarcomatoid features^7,9-11 and the evidence on how treat those cases remains limited.

Histologically characterized by the presence of an admixture of low grade bland tubules and spindle cells set in a mucinous stroma. However, it was realized that these tumors show resemblance to type 1 papillary RCC with both overlapping morphologic and immunohistochemistry features^12,13. At the molecular levels, a multi institutional study of 22 patients with MTSCC who underwent whole exome and transcriptome sequencing demonstrated that recurrent Hippo pathway alterations, low mutational burden and recurrent chromosomal loss represent the dominant molecular features of these tumors¹⁴.

In this retrospective study, we identified patients with MTSCC managed at our institutions between 2004 to 2018. The objectives of our study are to report on clinical presentations, genomic profile, survival and treatment outcomes of those patients.

Materials and methods

Study population:

Approval by the institutional review board was obtained to retrospectively identify patients with a diagnosis of MTSCC between 01/01/2004 to 06/01/2018 based on pathology reports within the institution database. In view of the rarity of this subtype and overlapping features with papillary RCC, all identified cases were submitted for further pathological confirmation by a dedicated genitourinary pathologist (Y.C.).

Data Collection:

Clinical data were extracted through individual retrospective chart reviews including patients’ demographics, clinical features, treatment details and survival outcomes. International Metastatic Renal Cell Carcinoma Database Consortium (IMDC) risk scores were calculated for patients with metastatic disease.

Clinical and statistical endpoints:

The entry point for analysis was from the date of first pathological diagnosis of MTSCC histology. Time to recurrence (TTR) with metastatic disease was calculated for patients who developed metastatic disease after undergoing nephrectomy in curative intent. Systemic therapy outcomes were described using time to treatment failure (TTF) analysis, defined as the interval between the date of initiating systemic therapy and the date of radiographic progression, drug cessation, or death, whichever occurred first, or censored at the last follow-up date. Radiographic progression was based on the interpretation of individual patient’s radiological reports by the treating Oncologist. Overall survival (OS) was calculated for all patients from the date of first pathological diagnosis of MTSCC histology until death, and patients who were still alive at the data cutoff were censored at the date of last follow-up. Median follow-up time was calculated from date of diagnosis among censored patients.

All statistical tests were 2-tailed, and P value <.05 was considered to indicate statistical significance. All analyses were performed with SAS version 9.3 software (SAS Institute, Cary, NC).

Molecular analysis

Next generation sequencing (NGS) was performed in 5 cases using the Memorial Sloan Kettering–Integrated Mutation Profiling of Actionable Cancer Targets (MSK-IMPACT™), briefly this is a hybridization capture technique of exons and introns of tumor with matched normal samples across 341, 441 and 468 genes which corresponds to the first three versions of the assay¹⁵. IHC for mismatch repair (MMR) proteins was performed in one case with underlying MLH1 deep deletion. Estimates of genome-wide total, allele-specific, and integer DNA copy number, were inferred from IMPACT sequencing data using the FACETS (Fraction and Allele-Specific Copy Number Estimates from Tumor Sequencing) algorithm (v0.5.6)¹⁶.

Results

Between 2004 to 2018, a total of 28 patients were initially identified from the pathology reports at our institution with a diagnosis of MTSCC. After further pathological confirmation, 3 patients were subsequently excluded as the diagnosis was inconclusive of MTSCC. The final data set included 25 patients and their baseline characteristic are summarized on Table 1. The median age at first pathological diagnosis with MTSCC was 58 years (range: 21, 74), with a female predominance (n=16, 64%). Symptoms at presentation were available for 21 patients, and most patients were asymptomatic at presentation (n=13, 62%) with one patient presenting with systemic symptoms who subsequently developed metastatic disease.

Table 1.

Patient characteristics (N=25)

	N	Median (range) or Frequency (%)	Quartile range for continuous variables
Age at diagnosis, years	25	58 (21, 74)	13.1
Female gender	16	64%
Primary tumor size, cm	22	5.7 (1.3, 16.2)	6
Primary stage	22
pT1	11	50%
pT2	8	36%
pT3a	2	9%
pT3b	1	5%
Symptoms at presentation	21
None	13	62%
Localized	7	33%
Systemic	1	5
Sarcomatoid features	2	8%
High grade features	5	25%
Primary tumor directed therapy	25
Radical nephrectomy	7	28%
Partial nephrectomy	16	64%
Ablation	2	8%
Metastatic disease	6	24%
Sites of metastases
Bone	4	67%
Lung	3	50%
Lymph nodes	2	33%
Brain	1	17%
Cutaneous	1	17%

All patients underwent primary tumor-directed therapy including nephrectomy in 23 patients (Radical, n=7, Partial, n=16) and cryoablation in 2 patients who both presented with small sized tumors on imaging (1.7 and 1.9 cm). Primary tumor pathological staging details were available in 22 out of the 23 patients who underwent nephrectomy. Most patients had small tumors with pathological T1 and T2 primary tumor staging in 11 patients (50%) and 8 patients (36%) respectively. Pathological T3 primary tumor staging was recognized in 3 patients who were also diagnosed with metastatic disease. High grade histological features were identified in 5 cases (20%) and 2 of those 5 patients also had evidence of sarcomatoid dedifferentiation.

Metastatic disease was identified in 6 patients, including 3 who presented with de novo metastatic disease and they all underwent cytoreductive nephrectomy. High grade histological features or sarcomatoid dedifferentiation were diagnosed in 5 of 6 patients with metastatic disease compared to 0 of 19 non-metastatic patients (83% vs 0%, p< 0.001, Fisher’s exact test). Most common sites of metastases included the bone (n=4, 67%) and lung (n=3, 50%). TTR with metastatic disease for the 3 patients who did not present with de novo metastatic disease and underwent nephrectomy in curative intent was 6.7, and 9.9 months in 2 patients with high grade histological features and 15.5 months in 1 patient who didn’t have any high grade histological features. IMDC risk parameters were available for 5 of the six metastatic case and were all in intermediate risk category.

Survival and treatment outcomes:

Survival outcomes for the entire cohort were favorable, with 3-year OS from first pathological diagnosis with MTSCC of 84.8% (95% CI: 59.6, 94.9) with a median follow-up time for survivors of 3.9 years (range:1 months, 10.3 years) (Figure 1). Three deaths occurred which were all from metastatic disease at 3.7, 15.0 and 29.2 months.

Figure 1. Overall survival of patients with MTSCC from first pathological diagnosis.

3-year overall survival from first pathological diagnosis with MTSCC was 84.8% (95% CI: 59.6, 94.9) for all patients with a median follow-up time for survivors of 3.9 years (range: 1 months, 10.3 years). Three deaths occurred which were all from metastatic disease at 3.7, 15.0 and 29.2 months.

Systemic therapy was initiated in 4 patients, details on duration of therapy of all lines of therapy are summarized on Figure 2. All 4 patients received first-line vascular endothelial growth factor tyrosine kinase inhibitor (VEGF-TKI) with sunitinib (n=2), pazopanib (n=1) and sorafenib (n=1), with a TTF of 30.6, 1.6, 3.0 and 3.8 months respectively. 3 patients received Anti-PD-1 checkpoint inhibitor therapy with single agent nivolumab in the third line setting, with TTF of 1.0, 2.4 and 4 months which were all discontinued due to progression of disease without any radiological disease response. Two of 4 metastatic patients who received systemic therapy are still alive and being considered for the next line of therapy, while the 2 other patients died from metastatic disease. Two other patients with metastatic disease didn’t receive any systemic therapy, including one patient who was managed with metastasectomy (right hemiarthroplasty and scalp lesion resection), and another patient who was unwell on presentation with brain metastasis and died at 3.7 months from diagnosis. Metastatic cases clinical features and treatment outcomes are detailed in the Supplementary Table.

Figure 2. Swimmers plot for treatment durations on all lines of therapy.

Details on all lines of systemic therapy per individual patients by coded by different colors. (*) Death from metastatic disease (†) Drug stopped due to disease progression.

Molecular features:

NGS with IMPACT™ was performed in 5 patients including 4 with metastatic disease. The tumor mutational burden was 0.0, 1.89, 4.10, 7.55 and 9.89 mutation/megabase. The most frequently altered gene was NF2 in 2 patients (40%) which is consistent with previous reports of common alterations in the Hippo pathway (Figure 3). Germline alterations were detected in 2 patients (40%) including CHEK2(T367Mfs*15) and BRCA2(S1982Rfs*22) mutation. The BRCA2 mutation was identified in a female patient of Ashkenazi Jewish descent and none of the 2 patients with germline mutations were diagnosed with another malignancy. One patient had evidence of MLH1 deep deletion on NGS, and subsequently IHC staining for MMR proteins showed loss of MLH1 and PMS2 expression consistent with deficient MMR status (dMMR) (Picture 1). The tumor of the patient who achieved long lived response on sunitinib harbored a total of 8 mutations including BAP1(I696T) missense mutation. FACETS analysis of 7 samples from 5 patients who underwent NGS identified loss of heterozygosity (LOH) of chromosomes 1,15 and 22 in 100% of cases and 6, 9 and 13 in 80% of cases and 14 in 60% of cases (Figure 4).

Figure 3.

Oncoprint illustrating most common Genomic alterations changes detected by NGS using MSK- IMPACT analysis across 5 patients with columns representing individual patients

Picture 1:

Immunohistochemistry staining for mismatch repair (MMR) proteins for one patient in the series with deficient.MMR status. Note for the loss of MLH1 and PMS2 in tumor cell.

Figure 4.

Allelic integer copy number as estimates by FACETS of 7 samples from 5 patients. HETLOSS (LOH) A=1; B=0, HOMDEL A=0, B=0, Gain A=2, B=1, Tetraploid A=2, B=2, AMP (or if broader high copy gain) A=3+, B=1, Copy number neutral LOH (CNLOH) A=2, B=0, Reciprocal LOH (RLOH) A=3+, B=0

Discussion:

MTSCC is a rare subtype of kidney cancer which was first recognized as a distinct entity in the WHO 2004 classification of renal neoplasms⁵. Multiple reports have described it as an indolent subtype with low grade histological features, low risk of metastases and favorable outcomes^6,8. Similar to other subtypes of RCC, cases with high grade histological and sarcomatoid dedifferentiation were previously reported and mostly in association with metastatic disease ^7,9,10. In light of the rarity of this subtype, limited cases were reported in the literature including ~ 13 metastatic cases and therefore it still remains not well defined. In this retrospective study, we studied outcomes of 25 patients with MTSCC managed at our institution and we found that the majority of patients presented with asymptomatic, low grade and localized tumors which were successfully treated with primary tumor directed therapy and overall achieved favorable survival outcomes. However, high grade histological features including high grade nuclear and sarcomatoid dedifferentiation were present in 20% of patients, and the presence of those features was strongly associated with development of metastatic disease (p< 0.001, Fisher’s exact test) with limited responses to standard metastatic RCC systemic therapy with the exception of one patient who achieved a long-lived response on sunitinib. Consistent with previous work most frequent molecular features included Hippo pathway mutations (40%) and multiple chromosomal losses¹⁴.

As described above, the overall survival for the entire cohort was favorable with 3-year overall survival rate of 84.8% over a median follow up time of 3.9 years (range:1 months, 10.3 years). However, we observed a distinct difference in outcomes between MTSCC of low and high grade histological features. Patients with low grade histological features presented with localized tumors with only 1 of 20 patients developing recurrent metastatic disease. While all 5 patients who had underlying high grade histological features developed or presented with metastatic disease. Most of the reported large series in the literature indicated that MTSCC is characterized by low grade, small sized and asymptomatic tumors ^6,7 although those series included ≤ 2 metastatic cases compared to 6 patients with metastatic disease in our study. Large studies demonstrated that the presence of high grade histological features in the common subtypes of RCC portends poorer prognosis ^17-19 which is consistent with our findings in this study.

With regards to systemic therapy for metastatic cases, 4 patients were treated with standard metastatic RCC systemic therapy with TTF of ≤ 6.0 months across different lines of therapy with the exception of one patient who achieved a long-lived response on first line sunitinib and progressed after staying on drug for 30.6 months. Three patients received nivolumab in the third line setting with TTF of ≤ 4.0 months with no disease response on imaging. Larkin et al ²⁰ previously reported a case with metastatic MTSCC treated with first line sunitinib and observed disease response at 12 weeks with continued clinical benefit from therapy at 24 weeks. As for nivolumab activity in this subtype, a series of 41 patients with metastatic non clear cell RCC who were treated with nivolumab included one patient with metastatic MTSCC who didn’t achieve radiological disease response and progressed after 6 months of therapy²¹. In view of the limited number of nivolumab treated metastatic cases with MTSCC and the lack of robust biomarkers of response it remains unclear whether nivolumab is an active treatment option for this disease. In light of the current available evidence, sunitinib seems to be an appropriate first line therapy in patients with advanced disease.

In our study, NGS with MSK-IMPACT™ was performed in 5 cases including 4 with metastatic disease both at the somatic and germline setting. Alterations in NF2 gene a member of the Hippo pathway was the most frequent somatic alteration in our cohort in 40% of patients. Using FACETS analysis on 5 cases who underwent NGS analysis, we observed consistent LOH mostly involving chromosomes 1, 6, 9, 13, 14, 15 and 22. Rakozy et al ⁸first observed unique and consistent chromosomal copy number losses among 6 MTSCC tumors involving chromosomes 1, 4, 6, 8, 9, 13, 14, 15, and 22. In an effort to define the molecular features of these tumors further, a multi-institutional cohort study analyzed tumors from 22 patients with MTSCC with both whole exome and transcriptome sequencing and identified that recurrent Hippo pathway alterations, low mutational burden and recurrent chromosomal loss represents the dominant features of these tumors¹⁴. However, both studies included non-metastatic cases while most patients in our study who underwent NGS had metastatic and high grade disease with similar genomic findings. Other interesting finding is the identification of germline alterations in 2 patients (40%) including CHEK2(T367Mfs*15) and BRCA2(S1982Rfs*22) mutations. Carlo et al²², recently reported on germline alterations across 254 patients with advanced RCC and demonstrated that 16.1% of patients harbored germline alterations including 10.5% in non–RCC-associated genes. In particular, CHEK2 germline mutations were overexpressed in patients with RCC compared to the general population suggestive of a potential role in the pathogenesis of RCC. The patient with germline BRCA2 mutation was of Ashkenazi Jewish origin and the significance of this finding in MTSCC is unknown. Although, we noted that on a previous reported case series of 15 patients with MTSCC one patient was diagnosed with both MTSCC and breast cancer⁶. Another unique finding is the identification of dMMR status in one patient based on IHC testing which is a very rare finding in RCC, and it could be prove to be of therapeutic significance in this patient as pembrolizumab is FDA approved for patients with unresectable or metastatic dMMR solid tumors that have progressed following prior treatment and who have no satisfactory alternative treatment options²³. Specific alterations including mutations in KDM5C and PBRM1 were shown to be associated with favorable outcomes on VEGF-TKI agents in patients with advanced clear cell RCC^24,25. The patient in our study who achieved an extreme response to sunitinib harbored a BAP1 mutation which is thought to have adverse outcomes on VEGF-TKI agents²⁵. Taken together, these findings support that patient with metastatic or high grade MTSCC could be considered for somatic and germline molecular genomic testing.

Some of the limitations of our study may include the small sized single center retrospective design, the lack of RECIST criteria assessment on patients treated with systemic therapy and the small number of patients within the study cohort who underwent molecular genomic testing.

Conclusions:

Our study supports previous findings of MTSCC as a disease of low grade potential and favorable outcomes. However, cases with high grade features have worse outcomes, therefore referral to centers of expertise and genomic molecular testing are encouraged for this group of patients.

Clinical practice points.

• MTSCC is a rare subtype of kidney cancer which is poorly defined with limited cases reported in the literature including ~ 13 metastatic cases.

• We studied cancer specifics outcomes and genomic features of 25 patients with MTSCC including 6 patients with metastatic disease.

• We found that the majority of patients presented with asymptomatic, low grade and localized tumors with favorable survival outcomes with 3-year overall survival rate of 84.8% for the entire cohort.

• High grade pathological features were identified in primary tumors from 5 patients (20%) and the presence of those features was strongly associated with metastatic disease (p<0.001, Fisher’s exact test).

• Four patients were treated with standard metastatic RCC systemic therapy with time to treatment failure ≤ 6 months across different agents including nivolumab with the exception of 1 patient who achieved long lived response on sunitinib after staying on drug for 30.6 months.

• Genomic features were studied in 5 patients including 4 metastatic cases and showed alterations in the hippo pathway in 2 patients which is similar to what is known in the non-metastatic setting. However, other diverse genomic features were identified including germline alterations in 2 patients, multiple chromosomal copy number losses and mismatch repair deficiency in 1 patient.