Sequence analysis and distribution of two new human cathepsin L splice variants

Low level lysosomal membrane permeabilization for limited release and sub-lethal functions of cathepsin proteases in the cytosol and nucleus

For a long time, lysosomes were purely seen as organelles in charge of garbage disposal within the cell. They destroy any cargo delivered into their lumen with a plethora of highly potent hydrolytic enzymes, including various proteases. In case of damage to their limiting membranes, the lysosomes release their soluble content with detrimental outcomes for the cell. In recent years however, this view of the lysosome changed towards acknowledging it as a platform for integration of manifold intra- and extracellular signals. Even impaired lysosomal membrane integrity is no longer considered to be a one-way street to cell death. Increasing evidence suggests that lysosomal enzymes, mainly cathepsin proteases, can be released in a spatially and temporarily restricted manner that is compatible with cellular survival. This way, cathepsins can act in the cytosol and the nucleus, where they affect important cellular processes such as cell division. Here, we review this evidence and discuss the routes and molecular mechanisms by which the cathepsins may reach their unusual destination.

Interfering with Host Proteases in SARS-CoV-2 Entry as a Promising Therapeutic Strategy

Due to its fast international spread and substantial mortality, the coronavirus disease COVID-19 evolved to a global threat. Since currently, there is no causative drug against this viral infection available, science is striving for new drugs and approaches to treat the new disease. Studies have shown that the cell entry of coronaviruses into host cells takes place through the binding of the viral spike (S) protein to cell receptors. Priming of the S protein occurs via hydrolysis by different host proteases. The inhibition of these proteases could impair the processing of the S protein, thereby affecting the interaction with the host-cell receptors and preventing virus cell entry. Hence, inhibition of these proteases could be a promising strategy for treatment against SARS-CoV-2. In this review, we discuss the current state of the art of developing inhibitors against the entry proteases furin, the transmembrane serine protease type-II (TMPRSS2), trypsin, and cathepsin L.

Differential roles of protease isoforms in the tumor microenvironment

Alternative splicing of precursor mRNA is a key mediator of gene expression regulation leading to greater diversity of the proteome in complex organisms. Systematic sequencing of the human genome and transcriptome has led to our understanding of how alternative splicing of critical genes leads to multiple pathological conditions such as cancer. For many years, proteases were known only for their roles as proteolytic enzymes, acting to regulate/process proteins associated with diverse cellular functions. However, the differential expression and altered function of various protease isoforms, such as (i) anti-apoptotic activities, (ii) mediating intercellular adhesion, and (iii) modifying the extracellular matrix, are evidence of their specific contribution towards shaping the tumor microenvironment. Revealing the alternative splicing of protease genes and characterization of their protein products/isoforms with distinct and opposing functions creates a platform to understand how protease isoforms contribute to specific cancer hallmarks. Here, in this review, we address cancer-specific isoforms produced by the alternative splicing of proteases and their distinctive roles in the tumor microenvironment.

Stress-resistant Translation of Cathepsin L mRNA in Breast Cancer Progression

The cysteine protease cathepsin L (CTSL) is often thought to act as a tumor promoter by enhancing tumor progression and metastasis. This goes along with increased CTSL activity in various tumor entities; however, the mechanisms leading to high CTSL levels are incompletely understood. With the help of the polyoma middle T oncogene driven breast cancer mouse model expressing a human CTSL genomic transgene, we show that CTSL indeed promotes breast cancer metastasis to the lung. During tumor formation and progression high expression levels of CTSL are maintained by enduring translation of CTSL mRNA. Interestingly, human breast cancer specimens expressed the same pattern of 5' untranslated region (UTR) splice variants as the transgenic mice and the human cancer cell line MDA-MB 321. By polyribosome profiling of tumor tissues and human breast cancer cells, we observe an intrinsic resistance of CTSL to stress-induced shutdown of translation. This ability can be attributed to all 5' UTR variants of CTSL and is not dependent on a previously described internal ribosomal entry site motif. In conclusion, we provide in vivo functional evidence for overexpressed CTSL as a promoter of lung metastasis, whereas high CTSL levels are maintained during tumor progression due to stress-resistant mRNA translation.

Post-transcriptional regulation of human cathepsin L expression

The expression of cathepsin L, a lysosomal protease, is known to be elevated in cancer and other pathologies. Multiple splice variants of human cathepsin L with variable 5'UTRs exist, which encode for the same protein. Previously we have observed that variant hCATL A (bearing the longest 5'UTR) was translated in vitro with significantly lower efficiency than variant hCATL AIII (bearing the shortest 5'UTR). Contrary to these findings, results of the present study reveal that in cancer cells, hCATL A mRNA exhibits higher translatability in spite of having lower stability than AIII. This is the first report demonstrating a highly contrasting trend in translation efficiencies of hCATL variants in rabbit reticulocytes and live cells. Expression from chimeric mRNAs containing 5'UTRs of A or AIII upstream to luciferase reporter cDNA established the A UTR to be the sole determinant for this effect. Transient transfections of bicistronic plasmids and mRNAs confirmed the presence of a functional Internal Ribosome Entry Site in this UTR. Our data suggest that differential stability and translation initiation modes mediated by the 5'UTRs of human cathepsin L variants are involved in regulating its expression.

Cathepsin L splice variants in human breast cell lines

Transcripts of the lysosomal cysteine proteinase cathepsin L are spliced into five variants (L-A, L-A1, LA-2, LA-3 and L-B), which have similar stabilities but different translation efficiencies, thus potentially yielding diverse amounts of the protein. The aim of this study was to investigate whether the abnormally elevated expression of cathepsin L in invasive tumours is due to overexpression of L-A3, the splice variant translated most efficiently. The expression pattern of cathepsin L mRNA variants was measured by quantitative polymerase chain reaction (qPCR) in two panels of cell lines obtained from precancerous and cancerous breast tissue. In both panels, the cell line exhibiting the highest in vitro invasiveness also expressed the highest amount of L-A3. Although the pattern of expression varied, the expression of the L-B variant was always remarkably lower than for other variants. We propose that posttranscriptional regulation of cathepsin L expression is altered during breast tumour progression.

Placental cathepsin M is alternatively spliced and exclusively expressed in the spongiotrophoblast layer

Cathepsin M and cathepsin-3 are cysteine peptidases expressed exclusively in the murine placenta. Their expression increases continuously from 11.5 dpc until the end of gestation. The cathepsin M gene consists of 8 exons and 7 introns covering 6 kb of genomic DNA on mouse chromosome 13. Multiple variants of CTSM were identified which display alternative splicing of exon 2 or exon 7. Alternative splicing of exon 2 does not affect the translated region of CTSM whereas aberrant splicing of exon 7 will results in enzymatically inactive versions of CTSM which still might retain inhibitory activity towards cysteine peptidases. Besides two defined major transcription start sites the putative promoter region comprises of a TATA-box and a relatively low (41%) G+C content reflecting its highly specific spatial and temporal expression pattern. Similar features are found within the promoter region of CTS3 which is highly homologous to CTSM. Both cathepsin M and -3 expression are confined to the spongiotrophoblast layer of the mouse placenta an expression pattern which is unique among cysteine peptidases located within the cluster of cathepsin J-like peptidases on mouse chromosome 13.

Transcription of human cathepsin L mRNA species hCATL B from a novel alternative promoter in the first intron of its gene

Cathepsin L is a lysosomal cysteine protease over-expressed in malignancy. It is very potent in degrading collagen, elastin, laminin and other components of the basement membrane and therefore, has been implicated in tumor invasion and metastasis. Two mRNA species, hCATL A and hCATL B, which contain an identical open reading frame and different 5'UTRs, were demonstrated to be encoded by the same gene located on chromosome 9q21-22. We have previously cloned and characterized the promoter responsible for the transcription of hCATL A (hCATL A promoter). However, it was not clear whether hCATL B is a splice variant of hCATL A or transcribed from a different promoter. In the present study, we demonstrate for the first time that hCATL B is transcribed from an alternate promoter (hCATL B promoter) located in the first intron of hCATL. This TATA-less promoter initiates transcription from two cytosine nucleotides present 191 and 367 bases upstream to the translation start codon. Deletion analysis revealed that the core promoter region lies upstream to these transcription initiation sites. This region contains several putative transcription factor-binding sites like AP-1, AP-4, GATA-1, Lmo2, NF-kappa B, MZF-1, NF-AT, etc. In U-87 MG cells, hCATL B promoter exhibits at least six times less activity than our previously characterized hCATL A promoter. However, this promoter is significantly more active in malignantly transformed cells as compared to its activity in untransformed cells. Thus, our results conclusively demonstrate that hCATL B mRNA is transcribed from an alternate promoter. Increased transcriptional activity from this promoter contributes to the elevated cathepsin L expression in transformed cells.

Family C1 cysteine proteases: biological diversity or redundancy?

Recent progress in the identification and partial characterization of novel genes encoding cysteine proteases of the papain family has considerably increased our knowledge of this family of enzymes. Kinetic data available to date for this large family indicate relatively broad, overlapping specificities for most enzymes, thus inspiring a growing conviction that they may exhibit functional redundancy. This is also supported in part by phenotypes of cathepsin knockout mice and suggests that several proteases can substitute for each other to degrade or process a given substrate. On the other hand, specific functions of one particular protease have also been documented. In addition, differences in cellular distribution and intracellular localization may contribute to defining specific functional roles for some of these proteases.

An alternatively spliced variant of cathepsin E in human gastric adenocarcinoma cells

Splice variant and authentic mRNAs for procathepsin E were measured at a ratio of 5:1 and 1:2 in Kato 3 and AGS cells, two human gastric adenocarcinoma cell lines. As a result of the precise splicing of the 3'-end of exon 6 to the 5'-end of exon 8, the variant lacked the 142 bp of exon 7 which encodes the second of the Asp residues that operate the catalytic mechanism of aspartic proteinases.

Identification and characterization of a novel human cathepsin L splice variant

Human cathepsin L (hCATL) has been implicated in a variety of physiological and pathological processes. It was hitherto known to be encoded by four mRNA species, namely hCATL A, AI, AII and hCATL B, differing in their 5' untranslated regions (UTRs). Of these, hCATL A, AI and AII are produced by the alternative splicing of the same primary transcript. HCATL AI and hCATL AII, lack 27 and 90 bases, respectively, from the 3' end of exon 1 of hCATL A. The present study describes the identification of a new splice variant hCATL AIII, which similarly lacks 145 bases from the 3' end of exon 1 of hCATL A. It is produced by the splicing out of 136-280 bases of the first exon in addition to intron 1 of hCATL A, which together serve as an intron for hCATL AIII. HCATL AIII was observed to be the most abundant splice variant in five different human cell lines. In vitro transcription coupled translation studies revealed that hCATL AIII is translated with 4.4-, 3.9- and 1.6-fold higher efficiency as compared to hCATL A, AI and AII, respectively. These results were further confirmed by measuring the enzymatic activities of the in vitro translated products. Cloning of hCATL AIII UTR upstream to luciferase reporter gene resulted in a 3.75-fold higher expression of the reporter gene as compared to the luciferase construct containing UTR of hCATL A. Thus, we have identified a novel human cathepsin L splice variant, hCATL AIII, which is most abundant in human cell lines and is translated with highest efficiency. Our results demonstrate either the presence of a positive or absence of a negative cis-acting regulatory element(s) in the UTR of hCATL AIII that is sufficient to confer translational advantage to a heterologous mRNA. The predominance of this most efficiently translated splice variant in malignant cells suggests that it plays a key role in the over-expression of human cathepsin L in cancer.

Lysosomal enzymes, cathepsins in brain tumour invasion

The expression patterns of different classes of peptidases in central nervous system (CNS) tumours have been most extensively studied in astrocytomas and meningiomas. Although the two types of tumours are very different in most respects, both may invade locally into normal brain. This process of invasion includes increased synthesis and secretion of lysosomal proteolytic enzymes - cathepsins. Aspartic endopeptidase cathepsin (Cat) D levels were found to be elevated in high-grade astrocytoma and partial inhibition of glioblastoma cell invasion by anti-Cat D antibody suggests that the enzyme activity is involved in the invasion process. Several studies on cysteine endopeptidase (CP) Cat B in gliomas agreed that transcript abundance, protein level and activity of Cat B increased in high-grade astrocytoma cultures compared with low-grade astrocytoma cultures and normal brain. Moreover, in glioma biopsies Cat B levels correlated with evidence of clinical invasion and it has been demonstrated that Cat B both in tumour cells and in endothelial cells can serve as a new biological marker for prognosis in glioblastoma patients. A high level of Cat B protein was also a diagnostic marker for invasive types of meningioma, distinguishing between histomorphologically benign, but invasive meningiomas and noninvasive, so-called clear-benign meningiomas. Cat L was also significantly increased in high-grade astrocytoma compared with low-grade astrocytoma and normal brain. Specific Cat L antibodies and antisense Cat L RNA transfection significantly lowered glioblastoma cell invasion. In meningioma, Cat L was a less-significant marker of invasion than Cat B. In contrast to cathepsins, the activities of endogenous cysteine peptidase inhibitors (CPIs), including stefins, cystatins and kininogens, were significantly higher in benign and atypical meningioma cell extracts than in malignant meningioma, and low-grade compared to high-grade astrocytoma. However, very low levels of stefins A and B were found in meningioma and glioblastoma tissues. Further studies on the expression levels and balance between cysteine endopeptidases (CPs) and CPIs would improve the clinical application of cathepsins in prognosis, which would lead to more-informed therapeutic strategies.

Cathepsin expression in oral squamous cell carcinoma: relationship with clinicopathologic factors

OBJECTIVE

Proteases are involved in the invasion and metastasis of carcinoma cells. In vivo, oral carcinoma cells easily invade the bone tissue and metastasize to the submandibular and neck lymph nodes. Cathepsin expression has been shown in some neoplastic tissues and serves as a prognostic indicator. The purpose of this study was to investigate the relationship between clinicopathohistologic grades and cathepsin expressions in oral squamous cell carcinoma and to investigate which cathepsin provides prognostic information for patients with oral carcinoma.

STUDY DESIGN

Immunohistochemical studies were performed on 78 carcinoma samples with monoclonal antibodies against cathepsins B, H, and L, and a polyclonal antibody against cathepsin D. Serial sections were stained by hematoxylin-eosin staining and classified by Anneroth's classification. Cathepsin B, H, L and D activities of blood serum were determined. Positive results indicative of the presence of cathepsin were investigated to determine any correlation between a particular cathepsin and histologic malignancy grades, tumor cell growth, serum cathepsin activities, and clinical factors.

RESULTS

Cathepsins B, H, L, and D were positive in every case. Although the labeling indices for cathepsins B (CB-LI), H (CH-LI), and D (CD-LI) for the cancer cases showed significant differences from those of controls, cathepsin L (CL-LI) of cancer cases showed no difference from that of controls (P <.05). A close correlation was found between CD-LI and T categories of TNM classification (P <.05), and between CD-LI and PCNA-LI (P <.05). Furthermore, a close correlation was found between CD-LI and N categories in TNM classification (P <.05). Pathologically, a close correlation was found between CB-LI or CD-LI and the pattern and/or stage of invasion (P <.05).

CONCLUSION

Cathepsin D and B expression were closely correlated with carcinoma invasion and progression. These proteases may be useful in determining the prognoses of patients with oral carcinoma.

Characterization of human cathepsin L promoter and identification of binding sites for NF-Y, Sp1 and Sp3 that are essential for its activity

Cathepsin L is a cysteine protease whose overexpression in human melanoma cells increases their tumorigenicity and switches their phenotype from non-metastatic to highly metastatic. Regulation of the transcription of the gene encoding human cathepsin L has not been yet studied and only preliminary data exist on the promoter regulation of the gene encoding rodent cathepsin L. In the present study we identified molecular elements involved in the transcriptional regulation of human cathepsin L in melanoma cells. The sequence of the 5'-flanking region of the gene encoding human cathepsin L was determined up to 3263 bp upstream of the translation start site. The major transcription intiation site was located. Three mRNA splice variants, differing in their 5' untranslated ends, were identified. Regulatory regions crucial for cathepsin L promoter activity were characterized between -1489 and -1646 bp. In this region, two GC boxes (-1590/-1595 and -1545/-1550) and a CCAAT motif (-1571/-1575) were involved in specific DNA-protein interactions. An electrophoretic mobility-shift assay demonstrated that Sp1 and Sp3 transcription factors bound to these GC boxes, and only the transcription factor nuclear factor Y (NF-Y) bound to the CCAAT motif. Mutagenesis studies demonstrated that these binding sites contributed at least 85% of cathepsin L promoter activity. Thus structural and functional analysis demonstrated that binding sites for NF-Y, Sp1 and Sp3 are essential for transcription of the gene encoding human cathepsin L in melanoma cells.

Splice variants of human cathepsin L mRNA show different expression rates

Human cathepsin L (hCATL) mRNA occurs in vivo in at least three splice variants. They differ in the length of exon 1, which comprises 278 nucleotides (hCATL-A), 188 nucleotides (hCATL-A2) and 132 nucleotides (hCATL-A3), respectively. We describe here the shortest variant for the first time. This form is predominant in all tissues and cells examined so far, including malignant tumors. We studied the expression rate of the three mRNA variants in order to explain why malignant kidney tumors show low cathepsin L activity despite of high mRNA levels. The variant hCATL-A3 showed the highest expression rate in vitro and in vivo. Based on these results, we suggest a cis-acting element on human cathepsin L mRNA which can be bound by a negative trans-acting regulator, thus leading to reduced expression rates.

Cloning and characterization of human cathepsin L promoter

Cathepsin L is a lysosomal cysteine protease, which is over-expressed and secreted by malignant cells. It is very potent in degrading collagen, elastin, laminin and other components of the basement membrane and, therefore, has been implicated in tumor invasion and metastasis. The structural portion of the human cathepsin L (hCATL) gene was cloned to elucidate its genomic organization (Chauhan et al., J. Biol. Chem. 218 (1993) 1039). In the present study, a 1.90 kb DNA fragment, containing 1825 bp of the 5' upstream region of hCATL and 75 bases of the first exon of the hCATL, was amplified by PCR from an adaptor ligated placental genomic library. This fragment has been demonstrated to exhibit promoter activity by luciferase reporter assays. Sequence analysis of this fragment revealed the presence of approximately 29 different putative transcription factor binding sites. Several of them like AP-4, GATA-1, Lmo2, CEBPB, MZF-1, NF-AT, etc. were present more than once in this region. However, a consensus CAAT box but no consensus TATA box was found within the 1.0 kb upstream of exon 1. The transcription initiation site of hCATL, using placental total RNA, was mapped to a single adenine residue 289 bases upstream of the ATG codon.

Male germ cells regulate transcription of the cathepsin l gene by rat Sertoli cells

It is well known that male germ cells regulate the steady state levels of numerous transcripts expressed by Sertoli cells. To date, however, there has been no direct test of whether this regulation reflects changes in gene transcription and/or transcript stability. This study used two experimental approaches to test the hypothesis that germ cells regulate transcription of the cathepsin L gene by rat Sertoli cells. We examined this gene because, in vivo, steady state levels of cath L messenger RNA in Sertoli cells change in a stage-specific manner as the surrounding germ cells progress through the 14 stages of the cycle of the seminiferous epithelium. In the first experimental approach, seminiferous tubules at stages VI-VII and stages IX-XII were incubated for 1 h in 4-thiouridine, and the amount of metabolically labeled cath L messenger RNA was quantified. The results demonstrate that transcription of the cath L gene by Sertoli cells is 7-fold higher at stages VI-VII than at stages IX-XII. The second experimental approach examined the ability of germ cells to regulate the activity of cath L reporter constructs in mature Sertoli cells. Before these studies, we isolated a cath L genomic clone and demonstrated that this clone contains the transcription start site of the cath L gene expressed by Sertoli cells. Transient transfection analysis then demonstrated that two reporter constructs, containing 244 and about 2.1 kb of sequence upstream from the transcription start site, had similar activities in mature Sertoli cells. However, germ cells only affected the activity of the larger construct in Sertoli cells, which was reduced by 30%. We conclude that germ cells regulate transcription of the cath L gene by Sertoli cells and that repressive effects of germ cells are mediated by elements upstream from nucleotide -244 of this gene.

Lysosomal cysteine proteases: more than scavengers

Lysosomal cysteine proteases were believed to be mainly involved in intracellular protein degradation. Under special conditions they have been found outside lysosomes resulting in pathological conditions. With the discovery of a series of new cathepsins with restricted tissue distributions, it has become evident that these enzymes must be involved in a range of specific cellular tasks much broader than as simple housekeeping enzymes. It is therefore timely to review and discuss the various physiological roles of mammalian lysosomal papain-like cysteine proteases as well as their mechanisms of action and the regulation of their activity.

Identification of an alternatively spliced seprase mRNA that encodes a novel intracellular isoform

Seprase is a homodimeric 170-kDa integral membrane gelatinase that is related to the ectoenzyme dipeptidyl peptidase IV. We have identified an alternatively spliced seprase messenger from the human melanoma cell line LOX that encodes a novel truncated isoform, seprase-s. The splice variant mRNA is generated by an out-of-frame deletion of a 1223-base pair exonic region that encodes part of the cytoplasmic tail, transmembrane, and the membrane proximal-central regions of the extracellular domain (Val(5) through Ser(412)) of the seprase 97-kDa subunit (seprase-l). The seprase-s mRNA has an elongated 5' leader (548 nucleotides) that harbors at least two upstream open reading frames that inhibit seprase-s expression from a downstream major open reading frame. Deletion mutagenesis of the wild type splice variant cDNA confirms that initiation of the seprase-s coding sequence begins with an ATG codon that corresponds to Met(522) of seprase-l. The seprase-s open reading frame encodes a 239-amino acid polypeptide with an M(r) approximately 27,000 that precisely overlaps the carboxyl-terminal catalytic region of seprase-l.

Identification of a splice variant of neutrophil collagenase (MMP-8)

We have identified a splice variant of human neutrophil collagenase (MMP-8) transcript (MMP-8alt) that has a 91 bp insertion between codons for amino acid residues 34 and 35 of MMP-8 cDNA. This splice variant encodes an open reading frame for a 444 residue protein, lacking a secretory signal sequence. Our data suggested that, as opposed to the original MMP-8, the translation product of MMP-8alt is not a secreted protein; nevertheless, it is enzymatically active. Further studies aimed at identifying the physiological substrates of MMP-8alt protein may lead to uncover novel roles it plays in cellular physiology.

Concentrations of lysosomal cysteine proteases are decreased in renal cell carcinoma compared with normal kidney

Renal cell carcinoma contains significantly lower concentrations of the lysosomal cysteine proteases, cathepsins B, C, H, L and S, than does normal kidney, as shown by several methods, such as activity determination, enzyme-linked immunosorbent assay, immunoblotting and immunohistochemistry. The same low levels of enzyme activity and concentration have been determined in renal cell carcinoma metastases in the lung. Our results on the decreased concentration of cysteine peptidases at the protein level would seem to conflict with earlier results on an increased concentration of the cathepsin L mRNA in renal cell carcinoma.